test trinity 2.9.1+galaxy2

[jennaj]

Reported error about a job that looks like it finished (from the logs) but failed.
Doesn't look like an input/param issue so far.

toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

[mvdbeek]

Results (powered by Planemo)

Summary

State	Count
Total	6
Passed	6
Error	0
Failure	0
Skipped	0

Passed s

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test tool test #1)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Left read files: $VAR1 = [
              'left_input.fastqsanger'
            ];
    Right read files: $VAR1 = [
              'right_input.fastqsanger'
            ];
    Wednesday, May 4, 2022: 16:44:15	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:44:15	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:44:16	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:44:16	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    ---------------------------------------------------------------
    ------------ In silico Read Normalization ---------------------
    -- (Removing Excess Reads Beyond 200 Coverage --
    ---------------------------------------------------------------
    
    # running normalization on reads: $VAR1 = [
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger'
              ],
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger'
              ]
            ];
    
    
    Wednesday, May 4, 2022: 16:44:16	CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G  --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger --pairs_together --PARALLEL_STATS  
    -prepping seqs
    Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger >> left.fa
    CMD: seqtk-trinity seq -A -R 2  /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger >> right.fa
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.ok
    CMD finished (0 seconds)
    Done converting input files.CMD: cat left.fa right.fa > both.fa
    CMD finished (0 seconds)
    CMD: touch both.fa.ok
    CMD finished (0 seconds)
    -kmer counting.
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------
    
    CMD: jellyfish count -t 56 -m 25 -s 100000000  both.fa
    CMD finished (0 seconds)
    CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
    CMD finished (0 seconds)
    CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
    CMD finished (0 seconds)
    CMD: touch jellyfish.K25.min2.kmers.fa.success
    CMD finished (0 seconds)
    -generating stats files
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > left.fa.K25.stats
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > right.fa.K25.stats
    -reading Kmer occurrences...
    -reading Kmer occurrences...
    
     done parsing 2541 Kmers, 2541 added, taking 0 seconds.
    
     done parsing 2541 Kmers, 2541 added, taking 0 seconds.
    STATS_GENERATION_TIME: 0 seconds.
    CMD finished (0 seconds)
    STATS_GENERATION_TIME: 0 seconds.
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.ok
    CMD finished (0 seconds)
    -sorting each stats file by read name.
    CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort
    CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> right.fa.K25.stats.sort
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    -defining normalized reads
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
    -opening left.fa.K25.stats.sort
    -opening right.fa.K25.stats.sort
    -done opening files.
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.ok
    CMD finished (0 seconds)
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
    100 / 100 = 100.00% reads selected during normalization.
    0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles.
    0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
    CMD finished (0 seconds)
    -search and capture.
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/left_input.fastqsanger
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452581/working/right_input.fastqsanger
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
    CMD finished (0 seconds)
    -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads
    
    
    Normalization complete. See outputs: 
    	/scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq
    	/scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq
    Wednesday, May 4, 2022: 16:44:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/normalization.ok
    Converting input files. (in parallel)Wednesday, May 4, 2022: 16:44:16	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
    Wednesday, May 4, 2022: 16:44:16	CMD: touch left.fa.ok
    Wednesday, May 4, 2022: 16:44:16	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
    Wednesday, May 4, 2022: 16:44:16	CMD: touch right.fa.ok
    Wednesday, May 4, 2022: 16:44:16	CMD: touch left.fa.ok right.fa.ok
    Wednesday, May 4, 2022: 16:44:16	CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa
    Wednesday, May 4, 2022: 16:44:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5358 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 5358
    Processed 5358 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 5358 vs. sorted list size: 5358
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_75475.thread_0
    Done opening file. tmp.iworm.fa.pid_75475.thread_1
    Done opening file. tmp.iworm.fa.pid_75475.thread_2
    Done opening file. tmp.iworm.fa.pid_75475.thread_3
    Done opening file. tmp.iworm.fa.pid_75475.thread_4
    Done opening file. tmp.iworm.fa.pid_75475.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:44:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100
    * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
    * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa  | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:44:19	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:44:19	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:44:19	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:44:19	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:44:19	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:44:19	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 8
    
    succeeded(1)   12.5% completed.    
    succeeded(2)   25% completed.    *****  PairPath Counts *****
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 496 has 1 pairpaths stored:
    	PairPath [_paths=[[496], []]] has read support: 44
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 496 has 1 pairpaths stored:
    	PairPath [_paths=[[496], []]] has read support: 44
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 558 has 1 pairpaths stored:
    	PairPath [_paths=[[558], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 558 has 1 pairpaths stored:
    	PairPath [_paths=[[558], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 559 has 1 pairpaths stored:
    	PairPath [_paths=[[559], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 559 has 1 pairpaths stored:
    	PairPath [_paths=[[559], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    
    succeeded(3)   37.5% completed.    
    succeeded(4)   50% completed.    
    succeeded(5)   62.5% completed.    
    succeeded(6)   75% completed.    
    succeeded(7)   87.5% completed.    
    succeeded(8)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:44:21	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:44:21	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:44:21	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452581/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 1, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525648, "src": "hdca"}]}, "paired_or_single": "unmerged_paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "No"}
    norm	"true"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test test against test.galaxyproject.org #2)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Left read files: $VAR1 = [
              'left_input.fastqsanger.gz'
            ];
    Right read files: $VAR1 = [
              'right_input.fastqsanger.gz'
            ];
    Wednesday, May 4, 2022: 16:45:15	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:45:15	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:45:16	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:45:16	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    ---------------------------------------------------------------
    ------------ In silico Read Normalization ---------------------
    -- (Removing Excess Reads Beyond 200 Coverage --
    ---------------------------------------------------------------
    
    # running normalization on reads: $VAR1 = [
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz'
              ],
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz'
              ]
            ];
    
    
    Wednesday, May 4, 2022: 16:45:16	CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G  --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz --right /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz --pairs_together --PARALLEL_STATS  
    -prepping seqs
    Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  <(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz) >> left.fa
    CMD: seqtk-trinity seq -A -R 2  <(gunzip -c /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz) >> right.fa
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.ok
    CMD finished (0 seconds)
    Done converting input files.CMD: cat left.fa right.fa > both.fa
    CMD finished (0 seconds)
    CMD: touch both.fa.ok
    CMD finished (0 seconds)
    -kmer counting.
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------
    
    CMD: jellyfish count -t 56 -m 25 -s 100000000  both.fa
    CMD finished (0 seconds)
    CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
    CMD finished (0 seconds)
    CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
    CMD finished (0 seconds)
    CMD: touch jellyfish.K25.min2.kmers.fa.success
    CMD finished (0 seconds)
    -generating stats files
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > left.fa.K25.stats
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > right.fa.K25.stats
    -reading Kmer occurrences...
    -reading Kmer occurrences...
    
     done parsing 2541 Kmers, 2541 added, taking 0 seconds.
    STATS_GENERATION_TIME: 
    0 done parsing  seconds.2541
     Kmers, 2541 added, taking 0 seconds.
    CMD finished (0 seconds)
    STATS_GENERATION_TIME: 0 seconds.
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.ok
    CMD finished (0 seconds)
    -sorting each stats file by read name.
    CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort
    CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> right.fa.K25.stats.sort
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    -defining normalized reads
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
    -opening left.fa.K25.stats.sort
    -opening right.fa.K25.stats.sort
    -done opening files.
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.ok
    CMD finished (0 seconds)
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
    100 / 100 = 100.00% reads selected during normalization.
    0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles.
    0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
    CMD finished (0 seconds)
    -search and capture.
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/left_input.fastqsanger.gz
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452582/working/right_input.fastqsanger.gz
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
    CMD finished (0 seconds)
    -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads
    
    
    Normalization complete. See outputs: 
    	/scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
    	/scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right_input.fastqsanger.gz.normalized_K25_maxC200_minC1_maxCV10000.fq
    Wednesday, May 4, 2022: 16:45:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/normalization.ok
    Converting input files. (in parallel)Wednesday, May 4, 2022: 16:45:16	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
    Wednesday, May 4, 2022: 16:45:16	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
    Wednesday, May 4, 2022: 16:45:16	CMD: touch left.fa.ok
    Wednesday, May 4, 2022: 16:45:16	CMD: touch right.fa.ok
    Wednesday, May 4, 2022: 16:45:16	CMD: touch left.fa.ok right.fa.ok
    Wednesday, May 4, 2022: 16:45:16	CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa
    Wednesday, May 4, 2022: 16:45:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5358 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 5358
    Processed 5358 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 5358 vs. sorted list size: 5358
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_189063.thread_0
    Done opening file. tmp.iworm.fa.pid_189063.thread_1
    Done opening file. tmp.iworm.fa.pid_189063.thread_2
    Done opening file. tmp.iworm.fa.pid_189063.thread_3
    Done opening file. tmp.iworm.fa.pid_189063.thread_4
    Done opening file. tmp.iworm.fa.pid_189063.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:45:16	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100
    * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
    * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa  | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:45:19	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:45:19	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:45:19	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:45:19	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:45:19	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:45:19	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 8
    
    succeeded(1)   12.5% completed.    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 257 has 1 pairpaths stored:
    	PairPath [_paths=[[257], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 257 has 1 pairpaths stored:
    	PairPath [_paths=[[257], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 218 has 1 pairpaths stored:
    	PairPath [_paths=[[218], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 218 has 1 pairpaths stored:
    	PairPath [_paths=[[218], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    
    succeeded(2)   25% completed.    
    succeeded(3)   37.5% completed.    
    succeeded(4)   50% completed.    
    succeeded(5)   62.5% completed.    
    succeeded(6)   75% completed.    
    succeeded(7)   87.5% completed.    
    succeeded(8)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:45:21	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:45:21	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:45:21	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452582/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 1, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525649, "src": "hdca"}]}, "paired_or_single": "unmerged_paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "No"}
    norm	"true"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger.gz"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test Test Prokka 1.14.6+galaxy1 #3)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Single read files: $VAR1 = [
              'input.fastqsanger'
            ];
    Wednesday, May 4, 2022: 16:02:33	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:02:34	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:02:34	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:02:34	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:02:34	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452562/working/input.fastqsanger | seqtk-trinity seq -A -R 1 - >> single.fa
    Wednesday, May 4, 2022: 16:02:34	CMD: touch single.fa.ok
    Wednesday, May 4, 2022: 16:02:35	CMD: touch single.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 3044 Kmers, 3044 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 3044
    Processed 3044 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 3044 vs. sorted list size: 3044
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_146740.thread_0
    Done opening file. tmp.iworm.fa.pid_146740.thread_1
    Done opening file. tmp.iworm.fa.pid_146740.thread_2
    Done opening file. tmp.iworm.fa.pid_146740.thread_3
    Done opening file. tmp.iworm.fa.pid_146740.thread_4
    Done opening file. tmp.iworm.fa.pid_146740.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:02:35	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/single.fa -f /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:02:35	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:02:35	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:02:35	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:02:35	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:02:35	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:02:35	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 3
    
    succeeded(1)   33.3333% completed.    
    succeeded(2)   66.6667% completed.    *****  PairPath Counts *****
    Node: 204 has 1 pairpaths stored:
    	PairPath [_paths=[[204], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 204 has 1 pairpaths stored:
    	PairPath [_paths=[[204], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    
    succeeded(3)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:02:38	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:02:38	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:02:38	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452562/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 1, "inputs": {"__current_case__": 0, "input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "unmerged_single_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "F"}}, "pool_mode": "No"}
    norm	"false"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test Test roary 3.13.0+galaxy2 #4)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Left read files: $VAR1 = [
              'left_input0.fastqsanger'
            ];
    Right read files: $VAR1 = [
              'right_input0.fastqsanger'
            ];
    Wednesday, May 4, 2022: 16:06:47	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:06:47	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:06:47	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:06:47	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    Converting input files. (in parallel)Wednesday, May 4, 2022: 16:06:47	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452572/working/left_input0.fastqsanger | seqtk-trinity seq -r -A -R 1 - >> left.fa
    Wednesday, May 4, 2022: 16:06:47	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452572/working/right_input0.fastqsanger | seqtk-trinity seq -A -R 2 - >> right.fa
    Wednesday, May 4, 2022: 16:06:47	CMD: touch right.fa.ok
    Wednesday, May 4, 2022: 16:06:47	CMD: touch left.fa.ok
    Wednesday, May 4, 2022: 16:06:47	CMD: touch left.fa.ok right.fa.ok
    Wednesday, May 4, 2022: 16:06:47	CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa
    Wednesday, May 4, 2022: 16:06:47	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5358 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 5358
    Processed 5358 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 5358 vs. sorted list size: 5358
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_271859.thread_0
    Done opening file. tmp.iworm.fa.pid_271859.thread_1
    Done opening file. tmp.iworm.fa.pid_271859.thread_2
    Done opening file. tmp.iworm.fa.pid_271859.thread_3
    Done opening file. tmp.iworm.fa.pid_271859.thread_4
    Done opening file. tmp.iworm.fa.pid_271859.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:06:48	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100
    * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
    * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa  | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:06:51	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:06:51	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:06:51	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:06:51	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:06:51	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:06:51	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 6
    
    succeeded(1)   16.6667% completed.    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 754 has 1 pairpaths stored:
    	PairPath [_paths=[[754], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 754 has 1 pairpaths stored:
    	PairPath [_paths=[[754], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 755 has 1 pairpaths stored:
    	PairPath [_paths=[[755], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 755 has 1 pairpaths stored:
    	PairPath [_paths=[[755], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 756 has 1 pairpaths stored:
    	PairPath [_paths=[[756], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 756 has 1 pairpaths stored:
    	PairPath [_paths=[[756], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    
    succeeded(2)   33.3333% completed.    
    succeeded(3)   50% completed.    
    succeeded(4)   66.6667% completed.    
    succeeded(5)   83.3333% completed.    
    succeeded(6)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:06:53	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:06:53	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:06:53	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452572/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 0, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "left_input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "paired", "right_input": {"values": [{"id": 96572750, "src": "hda"}]}, "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"}
    norm	"false"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Left read files: $VAR1 = [
              'left_input0.fastqsanger'
            ];
    Right read files: $VAR1 = [
              'right_input0.fastqsanger'
            ];
    Wednesday, May 4, 2022: 16:05:00	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:05:01	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:05:01	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:05:01	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    ---------------------------------------------------------------
    ------------ In silico Read Normalization ---------------------
    -- (Removing Excess Reads Beyond 200 Coverage --
    ---------------------------------------------------------------
    
    # running normalization on reads: $VAR1 = [
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger'
              ],
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger'
              ]
            ];
    
    
    Wednesday, May 4, 2022: 16:05:01	CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G  --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger --pairs_together --PARALLEL_STATS  
    -prepping seqs
    Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger >> left.fa
    CMD: seqtk-trinity seq -A -R 2  /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger >> right.fa
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.ok
    CMD finished (0 seconds)
    Done converting input files.CMD: cat left.fa right.fa > both.fa
    CMD finished (0 seconds)
    CMD: touch both.fa.ok
    CMD finished (0 seconds)
    -kmer counting.
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------
    
    CMD: jellyfish count -t 56 -m 25 -s 100000000  both.fa
    CMD finished (0 seconds)
    CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
    CMD finished (0 seconds)
    CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
    CMD finished (0 seconds)
    CMD: touch jellyfish.K25.min2.kmers.fa.success
    CMD finished (0 seconds)
    -generating stats files
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > left.fa.K25.stats
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > right.fa.K25.stats
    -reading Kmer occurrences...
    -reading Kmer occurrences...
    
     done parsing 2541 Kmers, 2541 added, taking 0 seconds.
    STATS_GENERATION_TIME: 0 seconds.
    
     done parsing 2541 Kmers, 2541 added, taking 0 seconds.
    CMD finished (0 seconds)
    STATS_GENERATION_TIME: 0 seconds.
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.ok
    CMD finished (0 seconds)
    -sorting each stats file by read name.
    CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort
    CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> right.fa.K25.stats.sort
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    -defining normalized reads
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
    -opening left.fa.K25.stats.sort
    -opening right.fa.K25.stats.sort
    -done opening files.
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.ok
    CMD finished (0 seconds)
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
    100 / 100 = 100.00% reads selected during normalization.
    0 / 100 = 0.00% reads discarded as likely aberrant based on coverage profiles.
    0 / 100 = 0.00% reads discarded as below minimum coverage threshold=1
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
    CMD finished (0 seconds)
    -search and capture.
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/left_input0.fastqsanger
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452563/working/right_input0.fastqsanger
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
    CMD finished (0 seconds)
    -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads
    
    
    Normalization complete. See outputs: 
    	/scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq
    	/scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger.normalized_K25_maxC200_minC1_maxCV10000.fq
    Wednesday, May 4, 2022: 16:05:01	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/normalization.ok
    Converting input files. (in parallel)Wednesday, May 4, 2022: 16:05:01	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
    Wednesday, May 4, 2022: 16:05:01	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
    Wednesday, May 4, 2022: 16:05:01	CMD: touch left.fa.ok
    Wednesday, May 4, 2022: 16:05:01	CMD: touch right.fa.ok
    Wednesday, May 4, 2022: 16:05:01	CMD: touch left.fa.ok right.fa.ok
    Wednesday, May 4, 2022: 16:05:01	CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa
    Wednesday, May 4, 2022: 16:05:01	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5358 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 5358
    Processed 5358 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 5358 vs. sorted list size: 5358
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_189047.thread_0
    Done opening file. tmp.iworm.fa.pid_189047.thread_1
    Done opening file. tmp.iworm.fa.pid_189047.thread_2
    Done opening file. tmp.iworm.fa.pid_189047.thread_3
    Done opening file. tmp.iworm.fa.pid_189047.thread_4
    Done opening file. tmp.iworm.fa.pid_189047.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:05:02	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100
    * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
    * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa  | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:05:04	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:05:04	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:05:04	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:05:04	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:05:04	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:05:04	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 8
    
    succeeded(1)   12.5% completed.    
    succeeded(2)   25% completed.    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 593 has 1 pairpaths stored:
    	PairPath [_paths=[[593], []]] has read support: 50
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 339 has 1 pairpaths stored:
    	PairPath [_paths=[[339], []]] has read support: 32
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 197 has 1 pairpaths stored:
    	PairPath [_paths=[[197], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 873 has 2 pairpaths stored:
    	PairPath [_paths=[[873], []]] has read support: 24
    	PairPath [_paths=[[873, 877], []]] has read support: 6
    
    Node: 875 has 1 pairpaths stored:
    	PairPath [_paths=[[875, 877], []]] has read support: 4
    
    Node: 877 has 1 pairpaths stored:
    	PairPath [_paths=[[877], []]] has read support: 68
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 474 has 1 pairpaths stored:
    	PairPath [_paths=[[474], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 474 has 1 pairpaths stored:
    	PairPath [_paths=[[474], []]] has read support: 38
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 475 has 1 pairpaths stored:
    	PairPath [_paths=[[475], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 475 has 1 pairpaths stored:
    	PairPath [_paths=[[475], []]] has read support: 40
    
    ## Total number of pairpaths: 1
    
    succeeded(3)   37.5% completed.    
    succeeded(4)   50% completed.    
    succeeded(5)   62.5% completed.    
    succeeded(6)   75% completed.    
    succeeded(7)   87.5% completed.    
    succeeded(8)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:05:07	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:05:07	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:05:07	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452563/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 0, "inputs": {"__current_case__": 1, "jaccard_clip": "false", "left_input": {"values": [{"id": 96572745, "src": "hda"}]}, "paired_or_single": "paired", "right_input": {"values": [{"id": 96572750, "src": "hda"}]}, "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"}
    norm	"true"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

• ✅ toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity (Test Test trinotate 3.2.2+galaxy0 #6)

  Command Line:

  Exit Code:

  • 0

  Standard Output:

  •      ______  ____   ____  ____   ____  ______  __ __
        |      ||    \ |    ||    \ |    ||      ||  |  |
        |      ||  D  ) |  | |  _  | |  | |      ||  |  |
        |_|  |_||    /  |  | |  |  | |  | |_|  |_||  ~  |
          |  |  |    \  |  | |  |  | |  |   |  |  |___, |
          |  |  |  .  \ |  | |  |  | |  |   |  |  |     |
          |__|  |__|\_||____||__|__||____|  |__|  |____/
    
        Trinity-v2.9.1
    
    
    
    Left read files: $VAR1 = [
              'left_input0.fastqsanger',
              'left_input1.fastqsanger'
            ];
    Right read files: $VAR1 = [
              'right_input0.fastqsanger',
              'right_input1.fastqsanger'
            ];
    Wednesday, May 4, 2022: 16:28:17	CMD: java -Xmx64m -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 0
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:28:17	CMD: java -Xmx4g -XX:ParallelGCThreads=2  -jar /usr/local/opt/trinity-2.9.1/util/support_scripts/ExitTester.jar 1
    Picked up _JAVA_OPTIONS:  -Xmx7g -Xms256m
    Wednesday, May 4, 2022: 16:28:17	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir
    Wednesday, May 4, 2022: 16:28:17	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis
    
    
    ----------------------------------------------------------------------------------
    -------------- Trinity Phase 1: Clustering of RNA-Seq Reads  ---------------------
    ----------------------------------------------------------------------------------
    
    ---------------------------------------------------------------
    ------------ In silico Read Normalization ---------------------
    -- (Removing Excess Reads Beyond 200 Coverage --
    ---------------------------------------------------------------
    
    # running normalization on reads: $VAR1 = [
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger',
                '/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger'
              ],
              [
                '/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger',
                '/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger'
              ]
            ];
    
    
    Wednesday, May 4, 2022: 16:28:18	CMD: /usr/local/opt/trinity-2.9.1/util/insilico_read_normalization.pl --seqType fq --JM 190G  --max_cov 200 --min_cov 1 --CPU 56 --output /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization --max_CV 10000  --SS_lib_type RF  --left /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger,/scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger --right /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger,/scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger --pairs_together --PARALLEL_STATS  
    -prepping seqs
    Converting input files. (both directions in parallel)CMD: seqtk-trinity seq -r -A -R 1  /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger >> left.fa
    CMD: seqtk-trinity seq -A -R 2  /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger >> right.fa
    CMD finished (0 seconds)
    CMD: seqtk-trinity seq -A -R 2  /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger >> right.fa
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: seqtk-trinity seq -r -A -R 1  /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger >> left.fa
    CMD finished (0 seconds)
    CMD: touch left.fa.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.ok
    CMD finished (0 seconds)
    Done converting input files.CMD: cat left.fa right.fa > both.fa
    CMD finished (0 seconds)
    CMD: touch both.fa.ok
    CMD finished (0 seconds)
    -kmer counting.
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer catalog from reads) --
    -------------------------------------------
    
    CMD: jellyfish count -t 56 -m 25 -s 100000000  both.fa
    CMD finished (0 seconds)
    CMD: jellyfish histo -t 56 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
    CMD finished (0 seconds)
    CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
    CMD finished (0 seconds)
    CMD: touch jellyfish.K25.min2.kmers.fa.success
    CMD finished (0 seconds)
    -generating stats files
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > left.fa.K25.stats
    CMD: /usr/local/opt/trinity-2.9.1/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25  --num_threads 28  > right.fa.K25.stats
    -reading Kmer occurrences...
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5337 added, taking 0 seconds.
    
     done parsing 5358 Kmers, 5337 added, taking 0 seconds.
    STATS_GENERATION_TIME: 0 seconds.
    STATS_GENERATION_TIME: 0 seconds.
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.ok
    CMD finished (0 seconds)
    -sorting each stats file by read name.
    CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> left.fa.K25.stats.sort
    CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/local/bin/sort --parallel=56 -k1,1 -T . -S 95G >> right.fa.K25.stats.sort
    CMD finished (0 seconds)
    CMD finished (0 seconds)
    CMD: touch left.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    CMD: touch right.fa.K25.stats.sort.ok
    CMD finished (0 seconds)
    -defining normalized reads
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
    -opening left.fa.K25.stats.sort
    -opening right.fa.K25.stats.sort
    -done opening files.
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.ok
    CMD finished (0 seconds)
    CMD: /usr/local/opt/trinity-2.9.1/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200  --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
    200 / 200 = 100.00% reads selected during normalization.
    0 / 200 = 0.00% reads discarded as likely aberrant based on coverage profiles.
    0 / 200 = 0.00% reads discarded as below minimum coverage threshold=1
    CMD finished (0 seconds)
    CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
    CMD finished (0 seconds)
    -search and capture.
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input0.fastqsanger
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/left_input1.fastqsanger
    -preparing to extract selected reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger ... done prepping, now search and capture.
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input0.fastqsanger
    -capturing normalized reads from: /scratch1/03166/xcgalaxy/main/staging/42452575/working/right_input1.fastqsanger
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
    CMD finished (0 seconds)
    CMD: ln -sf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq right.norm.fq
    CMD finished (0 seconds)
    -removing tmp dir /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/tmp_normalized_reads
    
    
    Normalization complete. See outputs: 
    	/scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
    	/scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right_input0.fastqsanger_ext_all_reads.normalized_K25_maxC200_minC1_maxCV10000.fq
    Wednesday, May 4, 2022: 16:28:18	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/normalization.ok
    Converting input files. (in parallel)Wednesday, May 4, 2022: 16:28:18	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/left.norm.fq | seqtk-trinity seq -r -A -R 1 - >> left.fa
    Wednesday, May 4, 2022: 16:28:18	CMD: cat /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/insilico_read_normalization/right.norm.fq | seqtk-trinity seq -A -R 2 - >> right.fa
    Wednesday, May 4, 2022: 16:28:18	CMD: touch left.fa.ok
    Wednesday, May 4, 2022: 16:28:18	CMD: touch right.fa.ok
    Wednesday, May 4, 2022: 16:28:18	CMD: touch left.fa.ok right.fa.ok
    Wednesday, May 4, 2022: 16:28:18	CMD: cat left.fa right.fa > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa
    Wednesday, May 4, 2022: 16:28:18	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa.ok
    -------------------------------------------
    ----------- Jellyfish  --------------------
    -- (building a k-mer (25) catalog from reads) --
    -------------------------------------------
    
    * Running CMD: jellyfish count -t 56 -m 25 -s 100000000 -o mer_counts.25.asm.jf /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa
    * Running CMD: jellyfish dump -L 1 mer_counts.25.asm.jf > jellyfish.kmers.25.asm.fa
    * Running CMD: jellyfish histo -t 56 -o jellyfish.kmers.25.asm.fa.histo mer_counts.25.asm.jf
    ----------------------------------------------
    --------------- Inchworm (K=25, asm) ---------------------
    -- (Linear contig construction from k-mers) --
    ----------------------------------------------
    
    * Running CMD: /usr/local/opt/trinity-2.9.1/Inchworm/bin//inchworm --kmers jellyfish.kmers.25.asm.fa --run_inchworm -K 25 --monitor 1   --num_threads 6  --PARALLEL_IWORM  -L 25  --no_prune_error_kmers  > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.tmp
    Kmer length set to: 25
    Min assembly length set to: 25
    Monitor turned on, set to: 1
    setting number of threads to: 6
    -setting parallel iworm mode.
    -reading Kmer occurrences...
    
     done parsing 5358 Kmers, 5358 added, taking 0 seconds.
    
    TIMING KMER_DB_BUILDING 0 s.
    -populating the kmer seed candidate list.
    Kcounter hash size: 5358
    Processed 5358 non-zero abundance kmers in kcounter.
    -Not sorting list of kmers, given parallel mode in effect.
    -beginning inchworm contig assembly.
    Total kcounter hash size: 5358 vs. sorted list size: 5358
    num threads set to: 6
    Done opening file. tmp.iworm.fa.pid_107126.thread_0
    Done opening file. tmp.iworm.fa.pid_107126.thread_1
    Done opening file. tmp.iworm.fa.pid_107126.thread_2
    Done opening file. tmp.iworm.fa.pid_107126.thread_3
    Done opening file. tmp.iworm.fa.pid_107126.thread_4
    Done opening file. tmp.iworm.fa.pid_107126.thread_5
    
    	Iworm contig assembly time: 0 seconds = 0 minutes.
    
    TIMING CONTIG_BUILDING 0 s.
    
    TIMING PROG_RUNTIME 0 s.
    * Running CMD: mv /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.tmp /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa
    Wednesday, May 4, 2022: 16:28:18	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa.finished
    --------------------------------------------------------
    -------------------- Chrysalis -------------------------
    -- (Contig Clustering & de Bruijn Graph Construction) --
    --------------------------------------------------------
    
    inchworm_target: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa
    bowtie_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa
    chrysalis_reads_fa: /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/filter_iworm_by_min_length_or_cov.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa 100 10 > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100
    * Running CMD: /usr/local/bin/bowtie2-build --threads 56 -o 3 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 1>/dev/null
    * Running CMD: bash -c " set -o pipefail;/usr/local/bin/bowtie2 --local -k 2 --no-unal --threads 56 -f --score-min G,20,8 -x /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/inchworm.fa.min100 /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa  | samtools view -@ 56 -F4 -Sb - | samtools sort -m 1821526308 -@ 56 -no - - > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam" 
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/scaffold_iworm_contigs.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm.bowtie.nameSorted.bam /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/GraphFromFasta -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa -r /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa -min_contig_length 200 -min_glue 2 -glue_factor 0.05 -min_iso_ratio 0.05 -t 56 -k 24 -kk 48  -strand  -scaffolding /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_scaffolds.txt  > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G  -k9,9gr /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted
    * Running CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted.wIwormNames
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/BubbleUpClustering -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/inchworm.fa  -weld_graph /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/iworm_cluster_welds_graph.txt.sorted -min_contig_length 200 -max_cluster_size 25  > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/CreateIwormFastaBundle -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/GraphFromIwormFasta.out -o /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -min 200
    * Running CMD: /usr/local/opt/trinity-2.9.1/Chrysalis/bin/ReadsToTranscripts -i /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/both.fa -f /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/bundled_iworm_contigs.fasta -o /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out -t 56 -max_mem_reads 50000000  -strand 
    * Running CMD: /usr/local/bin/sort --parallel=56 -T . -S 190G -k 1,1n /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/chrysalis/readsToComponents.out.sort
    Wednesday, May 4, 2022: 16:28:21	CMD: mkdir -p /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/read_partitions/Fb_0/CBin_0
    Wednesday, May 4, 2022: 16:28:21	CMD: touch /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/partitioned_reads.files.list.ok
    Wednesday, May 4, 2022: 16:28:21	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/write_partitioned_trinity_cmds.pl --reads_list_file /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/partitioned_reads.files.list --CPU 1 --max_memory 1G  --run_as_paired  --SS_lib_type F  --seqType fa --trinity_complete --full_cleanup  --no_version_check  --min_contig_length  200  --min_kmer_cov  1  --bflyHeapSpaceMax  190G --bfly_opts "-V 10 --stderr"  > recursive_trinity.cmds
    Wednesday, May 4, 2022: 16:28:21	CMD: touch recursive_trinity.cmds.ok
    Wednesday, May 4, 2022: 16:28:21	CMD: touch recursive_trinity.cmds.ok
    
    
    --------------------------------------------------------------------------------
    ------------ Trinity Phase 2: Assembling Clusters of Reads ---------------------
    ------- (involving the Inchworm, Chrysalis, Butterfly trifecta ) ---------------
    --------------------------------------------------------------------------------
    
    Wednesday, May 4, 2022: 16:28:21	CMD: /usr/local/opt/trinity-2.9.1/trinity-plugins/BIN/ParaFly -c recursive_trinity.cmds -CPU 56 -v -shuffle 
    Number of Commands: 8
    
    succeeded(1)   12.5% completed.    
    succeeded(2)   25% completed.    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 194 has 1 pairpaths stored:
    	PairPath [_paths=[[194], []]] has read support: 30
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 282 has 3 pairpaths stored:
    	PairPath [_paths=[[282], []]] has read support: 30
    	PairPath [_paths=[[282, 283, 284], []]] has read support: 6
    	PairPath [_paths=[[282, 283], []]] has read support: 2
    
    ## Total number of pairpaths: 3
    *****  PairPath Counts *****
    Node: 282 has 3 pairpaths stored:
    	PairPath [_paths=[[282], []]] has read support: 30
    	PairPath [_paths=[[282, 283, 284], []]] has read support: 6
    	PairPath [_paths=[[282, 283], []]] has read support: 2
    
    ## Total number of pairpaths: 3
    *****  PairPath Counts *****
    Node: 522 has 2 pairpaths stored:
    	PairPath [_paths=[[522], []]] has read support: 20
    	PairPath [_paths=[[522, 523], []]] has read support: 2
    
    Node: 523 has 1 pairpaths stored:
    	PairPath [_paths=[[523], []]] has read support: 16
    
    ## Total number of pairpaths: 3
    *****  PairPath Counts *****
    Node: 522 has 2 pairpaths stored:
    	PairPath [_paths=[[522], []]] has read support: 20
    	PairPath [_paths=[[522, 523], []]] has read support: 2
    
    Node: 523 has 1 pairpaths stored:
    	PairPath [_paths=[[523], []]] has read support: 16
    
    ## Total number of pairpaths: 3
    *****  PairPath Counts *****
    Node: 243 has 2 pairpaths stored:
    	PairPath [_paths=[[243], []]] has read support: 20
    	PairPath [_paths=[[243, 244, 245], []]] has read support: 4
    
    Node: 244 has 1 pairpaths stored:
    	PairPath [_paths=[[244, 245], []]] has read support: 2
    
    Node: 245 has 1 pairpaths stored:
    	PairPath [_paths=[[245], []]] has read support: 14
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 243 has 2 pairpaths stored:
    	PairPath [_paths=[[243], []]] has read support: 20
    	PairPath [_paths=[[243, 244, 245], []]] has read support: 4
    
    Node: 244 has 1 pairpaths stored:
    	PairPath [_paths=[[244, 245], []]] has read support: 2
    
    Node: 245 has 1 pairpaths stored:
    	PairPath [_paths=[[245], []]] has read support: 14
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 658 has 1 pairpaths stored:
    	PairPath [_paths=[[658], []]] has read support: 36
    
    Node: 653 has 1 pairpaths stored:
    	PairPath [_paths=[[653, 658], []]] has read support: 2
    
    Node: 655 has 2 pairpaths stored:
    	PairPath [_paths=[[655], []]] has read support: 8
    	PairPath [_paths=[[655, 656, 658], []]] has read support: 2
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 658 has 1 pairpaths stored:
    	PairPath [_paths=[[658], []]] has read support: 36
    
    Node: 653 has 1 pairpaths stored:
    	PairPath [_paths=[[653, 658], []]] has read support: 2
    
    Node: 655 has 2 pairpaths stored:
    	PairPath [_paths=[[655], []]] has read support: 8
    	PairPath [_paths=[[655, 656, 658], []]] has read support: 2
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 946 has 1 pairpaths stored:
    	PairPath [_paths=[[946], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 946 has 1 pairpaths stored:
    	PairPath [_paths=[[946], []]] has read support: 24
    
    ## Total number of pairpaths: 1
    *****  PairPath Counts *****
    Node: 945 has 1 pairpaths stored:
    	PairPath [_paths=[[945], []]] has read support: 8
    
    Node: 949 has 3 pairpaths stored:
    	PairPath [_paths=[[949], []]] has read support: 64
    	PairPath [_paths=[[949, 945], []]] has read support: 4
    	PairPath [_paths=[[949, 948], []]] has read support: 2
    
    ## Total number of pairpaths: 4
    *****  PairPath Counts *****
    Node: 945 has 1 pairpaths stored:
    	PairPath [_paths=[[945], []]] has read support: 8
    
    Node: 949 has 3 pairpaths stored:
    	PairPath [_paths=[[949], []]] has read support: 64
    	PairPath [_paths=[[949, 945], []]] has read support: 4
    	PairPath [_paths=[[949, 948], []]] has read support: 2
    
    ## Total number of pairpaths: 4
    
    succeeded(3)   37.5% completed.    
    succeeded(4)   50% completed.    
    succeeded(5)   62.5% completed.    
    succeeded(6)   75% completed.    
    succeeded(7)   87.5% completed.    
    succeeded(8)   100% completed.    
    
    All commands completed successfully. :-)
    
    
    
    ** Harvesting all assembled transcripts into a single multi-fasta file...
    
    Wednesday, May 4, 2022: 16:28:23	CMD: find /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/read_partitions/ -name '*inity.fasta'  | /usr/local/opt/trinity-2.9.1/util/support_scripts/partitioned_trinity_aggregator.pl --token_prefix TRINITY_DN --output_prefix /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.tmp
    -relocating Trinity.tmp.fasta to /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:28:23	CMD: mv Trinity.tmp.fasta /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta
    Wednesday, May 4, 2022: 16:28:23	CMD: /usr/local/opt/trinity-2.9.1/util/support_scripts/get_Trinity_gene_to_trans_map.pl /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta > /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta.gene_trans_map
    
    
    ###################################################################
    Trinity assemblies are written to /scratch1/03166/xcgalaxy/main/staging/42452575/working/trinity_out_dir/Trinity.fasta
    ###################################################################
    
    
    

  Job Parameters:

  • Job parameter	Parameter value
    pool	{"__current_case__": 0, "inputs": {"__current_case__": 2, "jaccard_clip": "false", "pair_input": {"values": [{"id": 1525647, "src": "hdca"}]}, "paired_or_single": "paired_collection", "strand": {"__current_case__": 1, "is_strand_specific": "true", "library_type": "RF"}}, "pool_mode": "Yes"}
    norm	"true"
    additional_params	{"guided": {"__current_case__": 0, "is_guided": "no"}, "long_reads": null, "min_contig_length": "200", "min_kmer_cov": "1"}
    __job_resource	{"__current_case__": 0, "__job_resource__select": "no"}
    chromInfo	"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"
    dbkey	"?"
    __input_ext	"fastqsanger"

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2

[jennaj]

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.9.1+galaxy2