Difference in log files for negatives when using gene_db

[kajcox]

Hi Kat, this is in reply to your email, but I have included the original query below also.

The files that are created are:
3__3-paired.gene_db.sam
3__3-paired.gene_db.sam.mod
3__3-paired.gene_db.unsorted.bam
3__genes__gene_db__results.txt
However the top 3 are empty and the genes results table just has the isolate number in it?

I've run 10 different genes using 10 different gene_db's now and have returned this error in the log file on a number of negatives - but a lot of them are also ones I'd expect to be negative. Sometimes when an isolate has a positive result at 90% and negative at 60% or vice versa and this log file error has been present it's indicated a file that needs to be re-run (I'm doing 1500 and the internet hamster in Sydney sometimes drops my VPN connection!) But a lot of them when I've rerun them have returned the same log file error and seem to be fine in all other aspects?

Many thanks in advance

Karen

Original query -
I am currently using SRST2 to map reads to target sequences using gene_db. I keep getting a difference in log files for my negatives? Some seem to run fine and return the usual but some of my log files are returning a message after the samtools portion which I have highlighted below.

I have run a different gene_db on this same isolate and not had this message turn up in the log file and similarly I have used the same gene_db.fasta file on different isolates and they seem to have worked fine?

Is this actually a run error and false negative or should I just assume this is a negative for the target sequence? Am I interpreting the log files incorrectly? The below message (2) occurs on the screen when the log files change also? I have tried forcing 0.1.18 version of samtools but this seems to have no effect?

Log file error
08/27/2015 04:47:29 program started
08/27/2015 04:47:29 command line: /local/software/python/2.7.5/bin/srst2 --input_pe /scratch/kc1e12/PhD/WAIT_trimmed/3-paired_1.fastq.gz /scratch/kc1e12/PhD/WAIT_trimmed/3-paired_2.fastq.gz --log$
08/27/2015 04:47:29 Total paired readsets found:1
08/27/2015 04:47:29 Index for gene_db.fasta is already built...
08/27/2015 04:47:29 Processing database gene_db.fasta
08/27/2015 04:47:29 Processing sample 3-paired
08/27/2015 04:47:29 Output prefix set to: 3__3-paired.gene_db
08/27/2015 04:47:29 Aligning reads to index gene_db.fasta using bowtie2...
08/27/2015 04:47:29 Running: bowtie2 -1 /scratch/kc1e12/PhD/WAIT_trimmed/3-paired_1.fastq.gz -2 /scratch/kc1e12/PhD/WAIT_trimmed/3-paired_2.fastq.gz -S 3__3-paired.gene_db.sam -q --very-sensi$
08/27/2015 04:48:28 Processing Bowtie2 output with SAMtools...
08/27/2015 04:48:28 Generate and sort BAM file...
08/27/2015 04:48:28 Running: samtools view -b -o 3__3-paired.gene_db.unsorted.bam -q 1 -S 3__3-paired.gene_db.sam.mod
08/27/2015 04:48:28 {'message': "Command 'samtools view -b -o 3__3-paired.gene_db.unsorted.bam -q 1 -S 3__3-paired.gene_db.sam.mod' failed with non-zero exit status: 1"}
08/27/2015 04:48:28 failed gene detection
08/27/2015 04:48:28 Tabulating results for database gene_db.fasta ...
08/27/2015 04:48:28 Finished processing for database gene_db.fasta ...
08/27/2015 04:48:28 Gene detection output printed to 3__genes__gene_db__results.txt
08/27/2015 04:48:28 SRST2 has finished.

2. Screen error
   ' is recognized as '*'.
   [main_samview] truncated file.

[katholt]

OK so if the sams/bams are empty but bowtie2 didn’t error out, it means no reads mapped to your database and it's a true negative.
We will add a check for 0 mapped reads to report this more clearly in future.

[kajcox]

Excellent news! Thanks Kat.
Best wishes
Karen
On 11/09/2015 6:29 AM, "Kat Holt" notifications@github.com wrote:

OK so if the sams/bams are empty but bowtie2 didn’t error out, it means no
reads mapped to your database and it's a true negative.
We will add a check for 0 mapped reads to report this more clearly in
future.

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