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
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.