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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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No such file - hg19.fa #16

Closed jollymrt closed 3 years ago

jollymrt commented 3 years ago

Hi, I am using the docker image to run IMSIndel. the command is

docker run imsindel --bam ./test_data_FT-5231103/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam --chr 22 --outd ./test_data_FT-5231103/ --reffa /Users/jshrivastava/IMSindel/test_data_FT-5231103/hg19.fa --indelsize 10000

I am getting the following error: /Users/jshrivastava/IMSindel/test_data_FT-5231103/hg19.fa: No such file.

However I can see the file in the specified directory: /Users/jshrivastava/IMSindel/test_data_FT-5231103 Domain Users 192B Jan 14 13:03 . Domain Users 352B Jan 13 16:43 .. Domain Users 1.9G Jan 13 16:22 FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam Domain Users 5.9M Jan 13 16:23 FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam.bai Domain Users 3.0G Aug 21 2018 hg19.fa Domain Users 3.5K Jan 14 13:03 hg19.fa.fai

What am I missing? Thanks for your help.

holrock commented 3 years ago

Hi, docker needs volume option for access local files. Try the command below.

docker run -v $PWD/test_data_FT-5231103:/test_data_FT-5231103 imsindel --bam /test_data_FT-5231103/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam --chr 22 --outd /test_data_FT-5231103/ --reffa /test_data_FT-5231103/hg19.fa --indelsize 10000

edit: update command

jollymrt commented 3 years ago

Thanks, it worked out well.

On Thu, Jan 14, 2021 at 5:28 PM holrock notifications@github.com wrote:

Hi, docker needs volume option for access other location files. Try the command below.

docker run -v /Users/jshrivastava/IMSindel/test_data_FT-5231103:/Users/jshrivastava/IMSindel/test_data_FT-5231103:ro imsindel --bam ./test_data_FT-5231103/FT-5231103_PRD_201205_A00284_0203_BHNYMMDSXY_IDTxGenIdp4C_BX-ES1166850_5231103_5231103_realigned_nodups.bam --chr 22 --outd ./test_data_FT-5231103/ --reffa /Users/jshrivastava/IMSindel/test_data_FT-5231103/hg19.fa --indelsize 10000

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/NCGG-MGC/IMSindel/issues/16#issuecomment-760584164, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATIKZSYR6ZKBXZHPDCWDPTSZ6K5XANCNFSM4WDDNQPQ .

-- Jolly Shrivastava Ph.D (Genetics, Genomics and Bioinformatics) University of California, Riverside

holrock commented 3 years ago

Previous master branch revision has bug at collecting fasta's results. please try current version.