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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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Failed to open the FASTA file effa #1

Closed zhangjianruwang closed 6 years ago

zhangjianruwang commented 6 years ago

hello, I got an error when using imsindel to call long deletion. About the dependencies: I use conda to install MAFFT and fasta3. for bioruby, I use apt-get install ruby-bio. the command I use to run imsindel is imsindel --chr chr18 --bam PV32_sorted_markdup.bam --outd ./results/ --indelsize 10000 -reffa hg19_bwa.fa 1>chr18_imsindel.log 2>chr18_imsindel.log

reffa( hg19_bwa) can be RWX for all users, and I have produce fai by samtools faidx.

The following lines are error log.

  1. detection of indels...

    paired long indel candidates: 77

    unpaired long indel candidates: 338

    short indel candidates: 4304

    [E::fai_build3] Failed to open the FASTA file effa Could not load fai index of effa /1/public_resources/softwares//IMSindel/lib/ims_indel/indel_detector.rb:91:in block in detect_indels': undefined methodjoin' for nil:NilClass (NoMethodError) from /1/public_resources/softwares//IMSindel/lib/ims_indel/indel_detector.rb:62:in each' from /1/public_resources/softwares/*/IMSindel/lib/ims_indel/indel_detector.rb:62:ineach_with_index' from /1/public_resources/softwares//IMSindel/lib/ims_indel/indel_detector.rb:62:in `detect_indels' from /1/public_resources/softwares//IMSindel/lib/ims_indel/indel_detector.rb:15:in indel_call' from /1/public_resources/softwares/*/IMSindel/lib/ims_indel.rb:90:inrun_detect_indels' from /1/public_resources/softwares//IMSindel/lib/ims_indel.rb:21:in `run' from /1/public_resources/softwares//IMSindel/bin/imsindel:43:in `

    '

holrock commented 6 years ago

Thank you for using our IMSindel. The error occurs by missing one hyphen of reffa option. The option is not -reffa, but --reffa.

zhangjianruwang commented 6 years ago

That was folly.

chenatf commented 6 years ago

Thanks for reply. The guy found his mistake after the software ran 10 hours, it is time-consuming to find the mistake. May you construct a static syntax analysis to quickly report the syntax mistake before the program starts running ?

holrock commented 6 years ago

Technically, while -reffa is valid syntax, that means --reffa effa. To avoid this time-consuming, we modify our program to confirm the existence of the file beforehand.

holrock commented 6 years ago

fix: 8e3f2ee73a37bce3797f1ddcc702e40a759deba2