Error when filtering reads:

[oriolfornes]

Hi, I have run the pipeline successfully for a few datasets. For others, however, the pipeline breaks during the filtering step.

Here is an example dataset that fails for me:

• SRAs: SRR1501142 SRR1501143 SRR1501144 SRR1501145 SRR1501146
• Sample: left ventricle
• Enzyme: HindIII
• Metadata file:

  SRR1501142  cf195000156b184c7e6bfbcb3848535d    R1  HindIII
  SRR1501143  cf195000156b184c7e6bfbcb3848535d    R1  HindIII
  SRR1501144  cf195000156b184c7e6bfbcb3848535d    R1  HindIII
  SRR1501145  cf195000156b184c7e6bfbcb3848535d    R1  HindIII
  SRR1501146  cf195000156b184c7e6bfbcb3848535d    R1  HindIII

• Error:

  $ cat cf195000156b184c7e6bfbcb3848535d/hi-c/runHiC-filtering.log 
  root                 main    @ 06/02/19 16:27:46: 
  # ARGUMENT LIST:
  # Sub-Command Name = filtering
  # Original Pairs = ./pairs-hg19/
  # MetaData = ./metadata.tsv
  # Genome Path = /sp3work/oriol/Hi-C/cf195000156b184c7e6bfbcb3848535d/data/hg19/hg19.fa
  # Stats Cache = allinone.cache
  # Temporary Dir = /sp1work/tmp/
  root                 main    @ 06/02/19 16:27:49: Filtered files will be saved under /sp3work/oriol/Hi-C/cf195000156b184c7e6bfbcb3848535d/hi-c/filtered-hg19
  root                 main    @ 06/02/19 16:27:49: Merge chunks ...
  root                 main    @ 06/02/19 16:27:49: Current SRA/FASTQ: SRR1501142 ...
  root                 main    @ 06/02/19 17:10:18: Done
  root                 main    @ 06/02/19 17:10:18: Current SRA/FASTQ: SRR1501143 ...
  root                 main    @ 06/02/19 17:54:18: Done
  root                 main    @ 06/02/19 17:54:18: Current SRA/FASTQ: SRR1501144 ...
  root                 main    @ 06/02/19 18:37:34: Done
  root                 main    @ 06/02/19 18:37:34: Current SRA/FASTQ: SRR1501145 ...
  root                 main    @ 06/02/19 19:19:29: Done
  root                 main    @ 06/02/19 19:19:29: Current SRA/FASTQ: SRR1501146 ...
  Traceback (most recent call last):
  File "/home/oriol/.conda/envs/tadpy/bin/runHiC", line 811, in <module>
  run(args, commands)
  File "/home/oriol/.conda/envs/tadpy/bin/runHiC", line 284, in run
  args.func(args, commands)
  File "/home/oriol/.conda/envs/tadpy/bin/runHiC", line 572, in filtering
  stats = collect_stats(inFiles)
  File "/home/oriol/.conda/envs/tadpy/lib/python3.6/site-packages/runHiC/filtering.py", line 32, in collect_stats
  merge_stats(stats_pool, list(stats_pool.keys()), 'pseudo')
  File "/home/oriol/.conda/envs/tadpy/lib/python3.6/site-packages/runHiC/filtering.py", line 161, in merge_stats
  stats_pool[outkey][i] += stats_pool[k][i]
  KeyError: '124_DanglingReads'

• Python:

  $ python --version
  Python 3.6.7

Thank you in advance!

[XiaoTaoWang]

Hi,

Thanks for your feedback! This is probably a bug for datasets with low sequencing depth, in which case not all SRAs can be detected with dangling reads. Can you try the latest version 0.8.3.post1 (https://pypi.org/project/runHiC/)?

Best!

[oriolfornes]

Updating to 0.8.3.post1 worked, thank you. I also wanted to thank you for your other great tools. Together, runHiC and TADLib are a powerful resource!