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nf-core / chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.
https://nf-co.re/chipseq
MIT License
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Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1) #355

Closed JiahuaQu closed 1 year ago

JiahuaQu commented 1 year ago

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

JoseEspinosa commented 1 year ago

Was this resolved when using the params-file as suggested here?

JiahuaQu commented 1 year ago

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

JoseEspinosa commented 1 year ago

Fixed as mentioned here