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

Closed chstellar closed 1 year ago

chstellar commented 1 year 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 1 year 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 1 year 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!