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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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Run time #19

Open jollymrt opened 3 years ago

jollymrt commented 3 years ago

I am running IMSIndel on docker as

docker run --rm -v /Users/jshrivastava/IMSindel/test_data_FT-5231103:/data imsindel --bam /data/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam --chr chr22 --outd /data --reffa /data/hg19.fa --indelsize 10000. --thread 6

I am running it on my mac book with 8gb ram and 1.4 GHz Quad-Core Intel Core i5 processor. Is it suppose to take this long? According to your paper it finished for all the chromosomes in 7.4 hrs.

IMSIndel runs the first 4 commands in 1/2 hour but then for the consensus reads sits forever. I had to kill it after 18 hrs.

  1. collecting indel related reads...done
  2. collecting unmapped reads... samtools view -F 1024 -f 8 /data/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam chr22 mate_unmapped_read_names: 661 samtools view -F 1024 -f 4 /data/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam chr22 Insert size Avg: 3101.651541157984 SD: 186181.5753257211

    unmapped reads: 1556

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

    backward clip with support reads: 3148

    forward clip with support reads: 3409

    non_clips with suport reads: 944

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

    backward clip with consensus: 3148 --> 2280

    forward clip with consensus: 3409 --> 2433

    shot indel with consensus: 944 --> 288

  7. making consensus seqs from support reads...done
  8. making consensus seq from B and F.. -- does not finish even after 18hrs.
holrock commented 3 years ago

In docker for mac, disk access is very slow. Changing the location of the temporary files may speed up the process.

for example: docker run --rm -v /Users/jshrivastava/IMSindel/test_data_FT-5231103:/data imsindel --bam /data/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam --chr chr22 --outd /data --reffa /data/hg19.fa --indelsize 10000. --thread 6 --temp /dev/shm