Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1)
JiahuaQu opened this issue · comments
Description of the bug
I submitted the job to run the nf-core chipseq in our institute's HPC, but the job always failed.
Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)'
Caused by:
Process NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1) terminated with an error exit status (1)
More details in the below and attachment.
It looks like that the BWA alignment had some issues.
Hope you can help figure out my errors. Thank you.
my_setting.config.txt
test.sh.txt
my.log
Command used and terminal output
No response
Relevant files
No response
System information
nextflow # version: 22.10.6
HPC
SGE
Singularity
CentOS
nf-core/chipseq v2.0.0
Was this resolved when using the params-file as suggested here?
I changed from BWA to bowtie2 which didn't not produce that error. I never tried BWA any more, so I don't know whether params-file will solve this problem. Becasue bowtie will produce new error as in my follow-up question in that thread of issue in your link, perhaps I can try to change back to BWA with params-file way? Or both aligners will have the same binding issue?
Later, I tried bwa and paras-file, but failed with error.
bwa_still_failed.txt
Fixed as mentioned here