tseemann/nullarbor

MakeFile:154: ref.fa.fai error 1

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#272 opened on Jun 18, 2020

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help wanted

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Description

Hi,

I ran nullarbor with the make ref.fa preview. It ran fine and then I ran

make again make

And got the the following error. Can enone provide me with information on it?

Cheers,

P

[16:25:20] Saving /media/psf/Home/IMRL_Sequencing/GB_EARS_Net_2019/ST_Catagories/Nullarbor/Output/nullarbor.log [16:25:20] Writing Makefile [16:25:20] Run the full pipeline with: [16:25:20] nice make all -j 3 -l 8 -C Output 2>&1 | tee -a Output/nullarbor.log [16:25:20] Done. (base) peter@ubuntu:/media/psf/Home/IMRL_Sequencing/GB_EARS_Net_2019/ST_Catagories/Nullarbor/Output$ make samtools faidx ref.fa [faidx] Could not build fai index ref.fa.fai make: *** [Makefile:154: ref.fa.fai] Error 1 (base) peter@ubuntu:/media/psf/Home/IMRL_Sequencing/GB_EARS_Net_2019/ST_Catagories/Nullarbor/Output$ make ref.fa make: 'ref.fa' is up to date. (base) peter@ubuntu:/media/psf/Home/IMRL_Sequencing/GB_EARS_Net_2019/ST_Catagories/Nullarbor/Output$ make samtools faidx ref.fa [faidx] Could not build fai index ref.fa.fai make: *** [Makefile:154: ref.fa.fai] Error 1 (base) peter@ubuntu:/media/psf/Home/IMRL_Sequencing/GB_EARS_Net_2019/ST_Catagories/Nullarbor/Output$

Contributor guide

Research direction
Verify that the reference FASTA file (ref.fa) exists and is not corrupt, and that samtools is installed and accessible. Check the Makefile to see what generates ref.fa.fai and if any dependencies are missing.
Tech stack
perl
Domain
backend
Issue type
Bug
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2
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Makesamtools
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50