shuf: end of file about chipseq_pipeline HOT 8 CLOSED

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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