Hi! Quite new to this, I am trying to run the scrna-seq pipline and I keep running into this error. I just wanted to run this piepline with the universc alignment tool on a small test.
Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 1.
The full error message was:
Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC (SRR12842503)'
Caused by:
Process `NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC (SRR12842503)` terminated with an error exit status (1)
Command executed:
universc \
--id 'sample-SRR12842503' \
-R1 SRR12842503_S1_L001_R1_001.fastq.gz -R2 SRR12842503_S1_L001_R2_001.fastq.gz \
--technology '10x' \
--chemistry 'auto' \
--reference cellranger_reference \
--description SRR12842503 \
--jobmode "local" \
--localcores 6 \
--localmem 36 \
--per-cell-data \
1> _log 2> _err
# save log files
echo !! > sample-SRR12842503/outs/_invocation
cp _log sample-SRR12842503/outs/_log
cp _err sample-SRR12842503/outs/_err
cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:UNIVERSC_ALIGN:UNIVERSC":
cellranger: $(echo $(cellranger count --version 2>&1 | head -n 2 | tail -n 1 | sed 's/^.* //g' | sed 's/(//g' | sed 's/)//g' ))
universc: $(echo $(bash /universc/launch_universc.sh --version | grep version | grep universc | sed 's/^.* //g' ))
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
.command.sh: line 16: sample-SRR12842503/outs/_invocation: No such file or directory
Work dir:
/var/tmp/pbs.9327528.pbs/work/65/67e2dbe50ffbc20f8701c774d19c1c
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
The directory it says it couldn't find, I thought that would be created by an internal program, not sure why it hasn't been created? Thanks so much for your answers!
Hi! Quite new to this, I am trying to run the scrna-seq pipline and I keep running into this error. I just wanted to run this piepline with the universc alignment tool on a small test.
This is the shell script I used
This was in the execution report file
The directory it says it couldn't find, I thought that would be created by an internal program, not sure why it hasn't been created? Thanks so much for your answers!