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NCGG-MGC / IMSindel

IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
https://www.nature.com/articles/s41598-018-23978-z
MIT License
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Error in running #24

Closed shaka-emperor closed 2 years ago

shaka-emperor commented 2 years ago

Hi, I got this error with no output and don't know why... Could you please help me?

Many thanks!

/home/IFNgroup/yejianyu/IMSindel/bin/imsindel --thread 30 --chr chr1 --bam ../../P1_NORM_GRCh38_HBV.sort.bam --outd P1_Norm --indelsize 10000 --reffa /home/IFNgroup/yejianyu/ref/bwa_build_index/GRCh38.fa

  1. collecting indel related reads... samtools view -F 1024 -f 2 ../../P1_NORM_GRCh38_HBV.sort.bam chr1

    backward_clips: 318998

    forward_clips: 317055

    non_clips: 1254149

  2. collecting indel related reads...done
  3. collecting unmapped reads... samtools view -F 1024 -f 8 ../../P1_NORM_GRCh38_HBV.sort.bam chr1 mate_unmapped_read_names: 37624 samtools view -F 1024 -f 4 ../../P1_NORM_GRCh38_HBV.sort.bam chr1 Insert size Avg: 297.33912158498964 SD: 70.2798480170345

    unmapped reads: 42986

  4. collecting unmapped reads...done
  5. considering support reads...

    backward clip with support reads: 12110

    forward clip with support reads: 7423

    non_clips with suport reads: 92888

  6. considering support reads...done
  7. making consensus seqs from support reads...

    backward clip with consensus: 12110 --> 4772

    forward clip with consensus: 7423 --> 3677

    shot indel with consensus: 92888 --> 50280

  8. making consensus seqs from support reads...done
  9. making consensus seq from B and F.. making consensus seq for long deletion...done
  10. detection of indels...

    paired long indel candidates: 335

    unpaired long indel candidates: 2688

    short indel candidates: 50280

    all_pos: 45676

    fin_indels: 45335

    samtools view -F 1024 -f 2 ../../P1_NORM_GRCh38_HBV.sort.bam chr1

    all_pos_depth 45676

    Traceback (most recent call last): 7: from /home/IFNgroup/yejianyu/IMSindel/bin/imsindel:44:in <main>' 6: from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel.rb:52:inrun' 5: from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel.rb:126:in run_detect_indels' 4: from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/indel_detector.rb:29:inindel_call' 3: from /home/IFNgroup/yejianyu/IMSindel/lib/ims_indel/indel_detector.rb:321:in final_indel_call' 2: from /home/yejianyu/anaconda3/lib/ruby/2.6.0/open-uri.rb:37:inopen' 1: from /home/yejianyu/anaconda3/lib/ruby/2.6.0/open-uri.rb:37:in `open'

holrock commented 2 years ago

Hi, could you check that P1_Norm directory exists?

shaka-emperor commented 2 years ago

Thanks a lot! And sorry to bother you again. My bam file has 32.5GB (average human WGS size), 5 threads, and detection of chromosome1 took me around 2.5 days. If I want to test all 24 chromosomes in one sample, it may cost one month... Is there any suggestions to accelerate the process? I like this software for its easy-to-use

holrock commented 2 years ago

--temp /dev/shm option runs faster than default option.

Unfortunately, IMSindel is slow. we use PC cluster for analysis.

shaka-emperor commented 2 years ago

Many thanks~