StarSolo 2.7.10b_alpha_220111, --soloCellReadStats Standard halts Solo running prematurely

[akhst7]

Hi,

I am using a following Solo script;

#!/opt/homebrew/bin/zsh

index=/Volumes/MySlateDrive/star_genome_index/index_human_10x
whitelist=/Volumes/MySlateDrive/10X_Whitelist/737K-arc-v1.txt
r1=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
r2=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
r3=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R1_001.fastq.gz
r4=/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R2_001.fastq.gz

STAR --genomeDir $index \
--runThreadN 40 \
--readFilesCommand 'gzip -c -d' \
--readFilesIn $r2,$r4 $r1,$r3 \
--soloCBwhitelist $whitelist \
--soloType CB_UMI_Simple \
--soloCBstart 1 \
--soloCBlen 16 \
--soloUMIstart 17 \
--soloUMIlen 12 \
--soloStrand Forward \
--soloBarcodeReadLength 0 \
--soloBarcodeMate 0 \
--clipAdapterType CellRanger4 \
--twopassMode Basic \
--soloMultiMappers EM \
--soloFeatures Gene GeneFull Velocyto \
--outFilterMultimapNmax 10 \
--outFilterScoreMin 30 \
--soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts \
--soloUMIfiltering MultiGeneUMI_CR \
--soloUMIdedup 1MM_CR \
--soloCellFilter  EmptyDrops_CR 5000 0.99 10 45000 90000  500  0.01  20000  0.01  10000 \
--outReadsUnmapped Fastx \
--outFileNamePrefix /Volumes/MySlateDrive/pbmc3Ksorted.GEX2 \
--outSAMtype None \
--soloCellReadStats Standard 

The presence of --soloCellReadStats Standard parameter stops Solo at 1st pass mapping with no clear error message as in a following output;

STAR --genomeDir /Volumes/MySlateDrive/star_genome_index/index_human_10x --runThreadN 40 --readFilesCommand "gzip -c -d" --readFilesIn /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz,/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R2_001.fastq.gz /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz,/Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L004_R1_001.fastq.gz --soloCBwhitelist /Volumes/MySlateDrive/10X_Whitelist/737K-arc-v1.txt --soloType CB_UMI_Simple --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloStrand Forward --soloBarcodeReadLength 0 --soloBarcodeMate 0 --clipAdapterType CellRanger4 --twopassMode Basic --soloMultiMappers EM --soloFeatures Gene GeneFull Velocyto --outFilterMultimapNmax 10 --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter EmptyDrops_CR 5000 0.99 10 45000 90000 500 0.01 20000 0.01 10000 --outReadsUnmapped Fastx --outFileNamePrefix /Volumes/MySlateDrive/pbmc3Ksorted.GEX2 --outSAMtype None --soloCellReadStats Standard
	STAR version: 2.7.10b_alpha_220111   compiled:  :/Users/akihikohoji/Downloads/Downloads/source
Jun 01 11:34:50 ..... started STAR run
Jun 01 11:34:50 ..... loading genome
Jun 01 11:35:28 ..... started 1st pass mapping

And a last part of log.out;

Sum of all Genome bytes: 5343458640
Sum of all SA bytes: 3109436257379
Sum of all SAi bytes: 185267190512
Processing splice junctions database sjdbN=362117,   pGe.sjdbOverhang=100
alignIntronMax=alignMatesGapMax=0, the max intron size will be approximately determined by (2^winBinNbits)*winAnchorDistNbins=589824
Created thread # 1
Starting to map file # 0
mate 1:   /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
mate 2:   /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
Starting to map file # 0
mate 1:   /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R2_001.fastq.gz
mate 2:   /Volumes/MySlateDrive/pbmc_granulocyte_sorted_3k/gex/pbmc_granulocyte_sorted_3k_S1_L003_R1_001.fastq.gz
Created thread # 2
Created thread # 3
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Created thread # 39

My system is as follows;

       
                 ,xNMM.          -----------------------------
               .OMMMMo           OS: macOS 13.4 22F66 arm64
               OMMM0,            Host: Mac13,2
     .;loddo:' loolloddol;.      Kernel: 22.5.0
   cKMMMMMMMMMMNWMMMMMMMMMM0:    Uptime: 3 hours, 28 mins
 .KMMMMMMMMMMMMMMMMMMMMMMMWd.    Packages: 208 (brew)
 XMMMMMMMMMMMMMMMMMMMMMMMX.      Shell: zsh 5.9
;MMMMMMMMMMMMMMMMMMMMMMMM:       Resolution: 3440x1440
:MMMMMMMMMMMMMMMMMMMMMMMM:       DE: Aqua
.MMMMMMMMMMMMMMMMMMMMMMMMX.      WM: Quartz Compositor
 kMMMMMMMMMMMMMMMMMMMMMMMMWd.    WM Theme: Blue (Dark)
 .XMMMMMMMMMMMMMMMMMMMMMMMMMMk   Terminal: iTerm2
  .XMMMMMMMMMMMMMMMMMMMMMMMMK.   Terminal Font: Monaco 10
    kMMMMMMMMMMMMMMMMMMMMMMd     CPU: Apple M1 Ultra
     ;KMMMMMMMWXXWMMMMMMMk.      GPU: Apple M1 Ultra
       .cooc,.    .,coo:.        Memory: 3467MiB / 131072MiB

[alexdobin]

Hi @akhst7

This is a bug, thanks for reporting it.
It only happens if --soloCellReadStats Standard --soloCellReadStats Standard are used together.
I will fix it soon.

[akhst7]

@alexdobin, Ok. Thanks.

[alexdobin]

Hi @akhst7

I have fixed the issue, please test it out:
https://github.com/alexdobin/STAR/releases/tag/STAR_2.7.10b_alpha_23-06-09
Thanks!

[akhst7]

@alexdobin, It works without any issues.

Thanks.