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Error in mapping: SAW-A10200: please give input file and output file #75

Closed chstellar closed 10 months ago

chstellar commented 11 months ago

I am running mapping on paired-end data. This is my .bcPara file:

in=/import/home/jyubq/PROJ_benchmarking/DAST_ss2022/SS200000135TL_D1.barcodeToPos.h5
in1=/import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_1.fq.gz
in2=/import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_2.fq.gz
barcodeReadsCount=/home/jyubq/PROJ_benchmarking/DAST_ss2022/73.trial/01.mapping/FP200003803_L01.barcodeReadsCount.txt
barcodeStart=0
barcodeLen=25
umiStart=25
umiLen=10
mismatch=1
bcNum=927081678 ## Input the first line from output of CIDCount
polyAnum=15
mismatchInPolyA=2
validCidFq=enable
outUnMappedFq=enable

And this is my command line instruction:

singularity exec /home/jyubq/DABS_ref/SAW/SAW_v6.1.sif mapping --outSAMattributes spatial --outSAMtype BAM SortedByCoordinate --genomeDir /home/jyubq/DABS_ref/genome/mus_musculus --runThreadN 16 --outFileNamePrefix /home/jyubq/PROJ_benchmarking/DAST_ss2022/73.trial/01.mapping/FP200003803_L01. --sysShell /bin/bash --stParaFile /home/jyubq/PROJ_benchmarking/DAST_ss2022/73.trial/01.mapping/FP200003803_L01.bcPara --readNameSeparator \" \" --limitBAMsortRAM 68582880124 --limitOutSJcollapsed 10000000 --limitIObufferSize=8011043863 --outBAMsortingBinsN 50 --outSAMmultNmax -1 > /home/jyubq/PROJ_benchmarking/DAST_ss2022/73.trial/01.mapping/FP200003803_L01.run.log

But I got this error: 

INFO:    Converting SIF file to temporary sandbox...
--- Error: [2023-11-1 9:58:12] SAW-A10200: please give input file and output file
bcSTAR: BarcodeMapping.cpp:483: bool STopt::SetOpt(const string&): Assertion `false' failed.
/usr/local/bin/mapping: line 1: 2036501 Aborted                 (core dumped) /opt/saw_v6.1.0_software/pipeline/mapping/bcSTAR $*
INFO:    Cleaning up image...

and my input files indeed exist:

<username>:<directory>$ ls /import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_1.fq.gz
/import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_1.fq.gz
<username>:<directory>$ ls /import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_2.fq.gz
/import/home/jyubq/PROJ_benchmarking/DAST_ss2022/FP200003803_L01_73_2.fq.gz

I am following the exact instructions given by the documentation, which does not give the output file. My SAW version is 06.1.2. Could anyone help with this?

Clouate commented 11 months ago

Hi, did you mount the disk where the input/output data are located when running singularity? If not, you could refer to the following code: singularity exec -B /path/to/data SAW_v6.1.sif mapping ... In your command, it should be: singularity exec -B /import,/home /home/jyubq/DABS_ref/SAW/SAW_v6.1.sif mapping ...

chstellar commented 10 months ago

Sorry for replying late. I found the issue was I did not refer to the .h5 input properly... It was a naming issue. Thank you for your help!