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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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no idr? #38

Closed jusu-E404 closed 7 years ago

jusu-E404 commented 7 years ago

Hello again, I'm running your pipeline with mm10 - it seems like the runs stop after peak calling with macs2, and idr never kicks in? I didn't include the "no_idr" option. Another note - all the intermediate files remain, no errors reported. Thanks!

leepc12 commented 7 years ago

Please post the error log (STDOUT) or an HTML report here. I need them for debugging. Did you get [TITLE]_report.html in your out_dir (./out by default)?

jusu-E404 commented 7 years ago

hi, yes. i'm attaching both. thanks!

leepc12 commented 7 years ago

Is the attached report the latest one? BDS generates such HTML report per run. Please look at HTML's filename and check timestamp of it to choose the latest one. MACS2 doesn't show up in the attached HTML report.

Your log says MACS2 peak calling is in progress but the last timestamp on the log is "INFO @ Sun, 26 Feb 2017 23:27:10". Please post the latest log here.

Did you get peaks on [out_dir]/peaks/macs2? Did you get [TITLE]_report.html in your out_dir (./out by default)?

jusu-E404 commented 7 years ago

Hi, yup its the latest one... I've noticed macs doesn't show too - I do get some peak files in macs2 directory - not all files are generated though: For rep1 I've got: .broadPeak, .gappedPeak, .narrowPeak, .pval0.1.broadPeak, pval0.1gappedPeak, and pval0.1.barrowPeak rep2 folder has only first 3 files. Pseudo_reps is only just partial (for rep1), nothing else was generated.

There is no html report in my out_dir. But there is still a folder with all the task..sh, and .stderr, .stdout and .exitCode files - the one with the last timestamp is id_57.sh... but there is no recorded error that I can see (not sure I'm looking at this right though).

I tried running this sample twice yesterday- both times it got stuck this way.. Not sure what can I try - I'm relatively new to all this - could something be wrong with my installation etc? Thanks again.

jusu-E404 commented 7 years ago

Ugh, ok. I've restarted my session and re-installed the dependencies again. Things are running fine and I'm past the point the pipeline was freezing on me earlier on.. No clue, maybe some of the modules didn't load or something. Apologies for the false alarm. Cheers.

leepc12 commented 7 years ago

No problem.

Please reopen this issue if the bug still persists.