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STOmics / SAW

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tissue.gef missing #101

Open Guy2Horev opened 2 months ago

Guy2Horev commented 2 months ago

Hello, I ran RNAseq scenario 3 and SAW exits with the following errcode. SAW-A70002: cannot access /home/ubuntu/STOmics/chip1Results/04.tissuecut/A02500D4.tissue.gef: No such file or directory could you please advice?

Clouate commented 2 months ago

Hi, could you provide your code and the log files?

Guy2Horev commented 2 months ago

Here is the command nohup bash ../stereoPipeline_v7.1.sh -sif ../SAW_7.1.sif -splitCount 1 -maskFile $dataDir/chip1/A02500D4.barcodeToPos.h5 -fq1 $dataDir/chip1/Lane1_1.fq.gz,$dataDir/chip1/Lane2_1.fq.gz,$dataDir/chip1/Lane3_1.fq.gz,$dataDir/chip1/Lane4_1.fq.gz -fq2 $dataDir/chip1/Lane1_2.fq.gz,$dataDir/chip1/Lane2_2.fq.gz,$dataDir/chip1/Lane3_2.fq.gz,$dataDir/chip1/Lane4_2.fq.gz -speciesName Dnaio_rerio -tissueType brain -refIndex $dataDir/reference/STAR_SJ100 -annotationFile $dataDir/reference/genomic.gtf -rRNAremove : N -threads 44 -outDir $outDir &

and this is the error message

[2024-04-18 17:13:29] SAW-A70002: cannot access /home/ubuntu/STOmics/chip1Results/04.tissuecut/A02500D4.tissue.gef: No such file or directo ry.

Clouate commented 2 months ago

@Guy2Horev Hi, it was because that the previous step, gene annotation(count) or tissue data extraction(tissueCut), was failed. You could check if the file, /home/ubuntu/STOmics/chip1Results/02.count/A02500D4.raw.gef and /home/ubuntu/STOmics/chip1Results/04.tissuecut/A02500D4.tissue.gef, exist. More log information could be found in the file nohup.out.