Comments (8)
No you don't have to start over. You can resume pipeline by simply running the same command on the working directory.
Yes, there was some update for the default.env
file. You need to move your current default.env
to somewhere and then git checkout default.env
and git pull
and then copy your default.env
back to the git directory.
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Thanks...the git problem is solved. But on resuming the pipeline I am still getting the "shuf: end of file" error at the same point, in this task: task.postalign_bed.subsample_tag_rep2.line_46.id_10
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Can you try with -no_random_source
?
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I tried and got same error. It seems that if I give -no-random-source in the "chipseq.py" command just after json-conf file, it is not being passed to the bds script. So from the bds it is printing "$no_random_source" as 'false'. Perhaps something needs to be set in the json conf file?
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fixed in commit 0ed5702
please git pull and try again with python chipseq.py --no-random-source
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Thanks !! That fixed the problem. Btw, just curious what is --no-random-source. Would it give the same result with or without that flag?
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With that flag --no-random-source
you will get slightly different result for pseudo replicates.
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--no-random-source
forces pipeline to make pseudo replicates without a specified random seed. So you will not get slightly different outputs for each pipeline run (even with the same inputs).
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Related Issues (20)
- aquas_chipseq pipline SPP error HOT 6
- Trimmed data-sets HOT 1
- Read length HOT 2
- "-q [SLURM_ACCOUNT_NAME]" interpreted as file HOT 1
- ERROR:root:--extsize must >= 1! HOT 2
- Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed. HOT 4
- [fread] Unexpected end of file (bwa_sai2sam_pe_core) HOT 6
- dead loop HOT 18
- job submission command HOT 2
- [Error] two same tag align file in (z)cat and shuf in pipe HOT 1
- Missing `-c` for `macs2 peakcall` ? HOT 1
- pipeline deprecated? HOT 2
- Can't download hg19 genome data HOT 2
- Some reps get ERROR:root:--extsize must >= 1! HOT 2
- Documentation for macs2? HOT 2
- Citing the AQUAS Pipeline HOT 1
- ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through HOT 25
- mm10 HOT 1
- JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa" HOT 1
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