Error related to snippy (samtools:[faidx] Could not build fai index reference/ref.fa.fai) - Githubissues

tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

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Error related to snippy (samtools:[faidx] Could not build fai index reference/ref.fa.fai) #278

Closed spencer411 closed 3 years ago

spencer411 commented 3 years ago

I do not get a report folder when running the pipeline, and have checked the install backward and forward. The error I get is as follows:

Error running command, check Isolate4/snippy/snps.log

Then I check the snps.log:

echo snippy 4.6.0

cd /network/rit/lab/andamlab/spencer/anthrax/nullarbor_test/OUTDIR

/network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/snippy --force --cpus 10 --outdir Isolate4/snippy --ref /network/rit/lab/andamlab/spencer/anthrax/nullarbor_test/anthrax.gb --R1 Isolate4/R1.fq.gz --R2 Isolate4/R2.fq.gz

samtools faidx reference/ref.fa

[faidx] Could not build fai index reference/ref.fa.fai

Note that I installed nullarbor with conda, no problem. Any help is appreciated