"hrc-1000g-check-bim.py" Unable to open specified bim file

Question

[zhangcc89]

Hi, I have met some problems about running hrc-1000g-check-bim.py. Can any experts give me some advice? Thanks very much.

Reference Panel:             HRC
Bim filename:                /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7
Reference filename:          /Volumes/GWAS_all2019/GWAS/pipe_QC_to_Phase_githb/_Chr/HRC.r1-1.GRCh37.wgs.mac5.sites.tab
Allele frequencies filename: iha_QCQC7
Chromosome flag set:         No
Allele frequency threshold:  0.2

***ERROR****: Unable to open specified bim file: /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7

Please check path and filename and try again

[ATpoint]

Isn't there a suffix missing? iha_QCQC7

[zhangcc89]

Nope. I have double checked.

[ATpoint]

I mean did you check that the file you find via ls /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7* is not actually called /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7.bim?

[zhangcc89]

The same errors with adding specified path:

Reference Panel:             HRC
Bim filename:                /Volumes/Mac8/GWAS_all/pipe_QC_to_Phase_githb/GWAS_Chr/iha_filter_QCQC7
Reference filename:          /Volumes/Mac8/GWAS_all/pipe_QC_to_Phase_githb/GWAS_Chr/HRC.r1-1.GRCh37.wgs.mac5.sites.tab
Allele frequencies filename: /Volumes/Mac8/GWAS_all/pipe_QC_to_Phase_githb/GWAS_Chr/iha_filter_QCQC7
Chromosome flag set:         No
Allele frequency threshold:  0.2

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

If you add new information, please update your initial question.

[WouterDeCoster]

Can you show the output of file /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7 and ls /Volumes/Mac8/GWAS_all20190509/GWAS/iha_QCQC7*?

Answer 1

[Tao]

Hi, I remember it needs to specify the suffix of bim file. Such as:

perl HRC-1000G-check-bim.pl -b data.bim -f data.frq -r HRC.r1-1.GRCh37.wgs.mac5.sites.tab -h

[zhangcc89]

Cool! Thanks very much.

[ATpoint]

Me: Isn't there a suffix missing? iha_QCQC7

You: Nope. I have double checked.

Didn't you say you checked if suffixing changes things? Please see my new comment above.

[WouterDeCoster]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.