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org.qcmg.picard.SAMFileReaderFactory keeps spawning processes #330

Open ZhaoxiangSimonCai opened 1 year ago

ZhaoxiangSimonCai commented 1 year ago

Describe the bug When I run the latest qmotif on WGS files, org.qcmg.picard.SAMFileReaderFactory seems to keep spawning processes, and then the program fails with Too many open files. The --threadargument doesn't seem to help in this case.

To Reproduce qmotif_cmd = "java -Xmx512G -jar /home/scai/tools/adamajava/qmotif/build/flat/qmotif.jar --threads 8 " \ f"--input-bam {BAM} " \ f"--input-bai {BAM}.bai " \ f"--log /home/scai/SangerTMM/qmotif-1.2/results_wgs/{cell_line}/{cell_line}.qmotif.log " \ "-ini /home/scai/SangerTMM/qmotif-1.2/config.ini " \ f"-output-xml /home/scai/SangerTMM/qmotif-1.2/results_wgs/{cell_line}/{cell_line}.xml " \ f"-output-bam /home/scai/SangerTMM/qmotif-1.2/results_wgs/{cell_line}/{cell_line}.telomere.bam"

Screenshots image

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Additional context I could run qmotif successfully on WES data. SAMFileReaderFactory also spawns many processes but it was able to finish properly.

Thank you so much for your help!

ChristinaXu2017 commented 1 year ago

Based on your error message, the program died before reaching the thread step. Could I have look at your ini file? I doubt there may be too many [INCLUDES] regions.

ZhaoxiangSimonCai commented 1 year ago

Thank you for your reply Christina. I'm using the default [INCLUDES] regions from your documentation page.

[PARAMS] stage1_motif_regex=(TTAGGG.TTAGGG.TTAGGG.TTAGGG)|(CCCTAA.CCCTAA.CCCTAA.CCCTAA) ;stage1_string_rev_comp=true stage2_motif_regex=(...GGG){2,}|(CCC...){2,} window_size=10000 [INCLUDES] ; name, regions (sequence:start-stop) chr1p chr1:10001-12464 chr1q chr1:249237907-249240620 chr2p chr2:10001-12592 chr2q chr2:243187373-243189372 chr2xA chr2:243150480-243154648 chr3p chr3:60001-62000 chr3q chr3:197960430-197962429 chr3xB chr3:197897576-197903397 chr4p chr4:10001-12193 chr4q chr4:191041613-191044275 chr5p chr5:10001-13806 chr5q chr5:180903260-180905259 chr6p chr6:60001-62000 chr6q chr6:171053067-171055066 chr7p chr7:10001-12238 chr7q chr7:159126558-159128662 chr8p chr8:10001-12000 chr8q chr8:146302022-146304021 chr9p chr9:10001-12359 chr9q chr9:141151431-141153430 chr10p chr10:60001-62000 chr10q chr10:135522469-135524746 chr11p chr11:60001-62000 chr11q chr11:134944458-134946515 chr12p chr12:60001-62000 chr12q chr12:133839458-133841894 chr12xC chr12:93158-97735 chr13p chr13:19020001-19022000 chr13q chr13:115107878-115109877 chr14p chr14:19020001-19022000 chr14q chr14:107287540-107289539 chr15p chr15:20000001-20002000 chr15q chr15:102518969-102521391 chr16p chr16:60001-62033 chr16q chr16:90292753-90294752 chr17p chr17:1-2000 chr17q chr17:81193211-81195210 chr18p chr18:10001-12621 chr18q chr18:78014226-78017247 chr19p chr19:60001-62000 chr19q chr19:59116822-59118982 chr20p chr20:60001-62000 chr20q chr20:62963520-62965519 chr21p chr21:9411194-9413193 chr21q chr21:48117788-48119894 chr22p chr22:16050001-16052000 chr22q chr22:51242566-51244565 chrXp chrX:60001-62033 chrXq chrX:155257733-155260559 chrYp chrY:10001-12033 chrYq chrY:59360739-59363565

Also I tried running qmotif on the WGS data of another sample that has deeper sequencing coverage, and it actually worked well. Could it be something that's in the bam file that causes this issue?

ChristinaXu2017 commented 1 year ago

I am also curious why you ask for so much RAM. this tool is not RAM-hungry. I just ran on my own WGS data with the same ini file. It works fine.

ChristinaXu2017 commented 1 year ago

Your error happens during reading the BAM file with a provided index file. It is possible something wrong with the index file or the BAM file. Alternatively, make sure the file is not moving during qmotif running.

ZhaoxiangSimonCai commented 1 year ago

Our server has enough RAM so I set it to 512G just in case. Changing to 32G does not solve the problem. No file is moving during running qmotif. I tried to index the bam again but it is still the same.

Is it possible to provide more details about where the error happens, and what could be wrong? From simply viewing the BAM I can't see any problem.

ChristinaXu2017 commented 1 year ago

It seems qmotif works well with WES BAMs and some WGS BAM, but throw the exception "Too many open files" for some WGS BAMs. I just test it with a 38G WGS BAM with 4 threads, and the run was completed in less than 10 minutes. The INI file is from our document page as well. I am also sure your problem is nothing to do with the "thread" option. your error happens before the parallel jobs are called. Because I can't test your particular BAM file, only based on the screenshot message and our code investigation, the exception says "FileNotFound", so I guess it may be caused by:

  1. The running environment issue, such as file updating, opening file handle number limits, permission issues, etc.
  2. BAM file issues, such as uncorrected BAM file header, and dated index file, which tools created index file, etc.
  3. hardware issues, such as I/O connection issues, RAM, cache, etc.

I am sorry that I really can't provide strong opinions without a real testing dataset.

ZhaoxiangSimonCai commented 1 year ago

Thanks again. I managed to run qmotif with setting includes_only=true in the config. I couldn't find much about this parameter on your documentation website or paper. Could you please help explain the difference if possible? I thought qmotif always only looked at the specified regions?