MakeFile:154: ref.fa.fai error 1

[peflanag]

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$

[peflanag]

Hey @tseemann I just noticed you self assigned this. Just wondering if you've seen this before?

Cheers,

Peter

[peflanag]

Just an update, I ran nullarbor with fewer samples and C. diff this time and it worked fine. So i tried this original run again (saureus) but the same error. It's like it isn't making the ref.fa.fai file. But its weird that its only happening for my saureus samples.