Open jalalsiddiqui opened 3 years ago
byee4
commented
3 years ago random contigs were likely trimmed from the clipper references - if it encounters a region that doesn't exist in the reference it might complain. You can see which chromosomes are included for each supported species (eg you can get a unique list of valid chromosomes from hg19 gencode v19 (hg19_exons.bed) using some bash:
awk -F "\t" '{print $1}' hg19_exons.bed | uniq
jalalsiddiqui
commented
3 years ago Thank you so much!
I will look into this.
Jalal
From: Brian Yee notifications@github.com Sent: Friday, January 22, 2021 5:35 PM To: YeoLab/clipper clipper@noreply.github.com Cc: Jalal K. Siddiqui siddiqui.13@osu.edu; Author author@noreply.github.com Subject: Re: [YeoLab/clipper] Invalid contig error (#93)
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random contigs were likely trimmed from the clipper references - if it encounters a region that doesn't exist in the reference it might complain. You can see which chromosomes are included for each supported species (eg you can get a unique list of valid chromosomes from hg19 gencode v19 (hg19_exons.bed) using some bash:
link to clipper data/regionshttps://urldefense.com/v3/__https://github.com/YeoLab/clipper/tree/master/clipper/data/regions__;!!KGKeukY!i75ETm_4UTpK_2-5zIyLGXSrLXvM1LXckRx_L6aWs1UEQoameqwZXbencRyV8ug70is$
awk -F "\t" '{print $1}' hg19_exons.bed | uniq
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jalalsiddiqui
commented
3 years ago I ran this for around ~10 hours but I had no output or anything occur. Do you know what the problem might be?
byee4
commented
3 years ago I have seen Clipper run for longer than that, we allow 24 hours per run although the vast majority of jobs don't take that long.
jalalsiddiqui
commented
3 years ago Thanks. Is there a way to make this run faster?
Jalal
From: Brian Yee notifications@github.com Sent: Tuesday, January 26, 2021 4:45 PM To: YeoLab/clipper clipper@noreply.github.com Cc: Jalal K. Siddiqui siddiqui.13@osu.edu; Author author@noreply.github.com Subject: Re: [YeoLab/clipper] Invalid contig error (#93)
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I have seen Clipper run for longer than that, we allow 24 hours per run although the vast majority of jobs don't take that long.
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byee4
commented
3 years ago I've had some success running it on an ec2 instance with more cores, c3.8xlarge for instance might speed it up some.
jalalsiddiqui
commented
3 years ago I use cluster computing. I can try to increase the number of threads.
Jalal
From: Brian Yee notifications@github.com Sent: Tuesday, January 26, 2021 6:48 PM To: YeoLab/clipper clipper@noreply.github.com Cc: Jalal K. Siddiqui siddiqui.13@osu.edu; Author author@noreply.github.com Subject: Re: [YeoLab/clipper] Invalid contig error (#93)
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I've had some success running it on an ec2 instance with more cores, c3.8xlarge for instance might speed it up some.
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jalalsiddiqui
commented
3 years ago I am running the pipeline with 6 threads at the moment. Note I am doing a single end analysis with the first read only.
jalalsiddiqui
commented
3 years ago One more question. Is there a way to monitor progress. There is no output so I am not sure of the progress I am making on the peak calling.
Traceback (most recent call last): File "/users/PAS1143/osu8165/.conda/envs/clipper3/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, **kwds)) File "/users/PAS1143/osu8165/.conda/envs/clipper3/lib/python3.7/site-packages/clipper/src/call_peak.py", line 932, in call_peaks subset_reads = list(bam_fileobj.fetch(reference=str(interval.chrom), start=interval.start, end=interval.stop)) File "pysam/libcalignmentfile.pyx", line 1081, in pysam.libcalignmentfile.AlignmentFile.fetch File "pysam/libchtslib.pyx", line 686, in pysam.libchtslib.HTSFile.parse_region ValueError: invalid contig
sys.exit(call_main())
File "/users/PAS1143/osu8165/.conda/envs/clipper3/lib/python3.7/site-packages/clipper/src/main.py", line 266, in call_main
main(options)
File "/users/PAS1143/osu8165/.conda/envs/clipper3/lib/python3.7/site-packages/clipper/src/main.py", line 105, in main
peaks_dicts.append(job.get(timeout=options.timeout))
File "/users/PAS1143/osu8165/.conda/envs/clipper3/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
ValueError: invalid contig
chr1_KI270708v1_random""" The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/users/PAS1143/osu8165/.conda/envs/clipper3/bin/clipper", line 8, inchr1_KI270708v1_random