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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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No report folder in OUTDIR [Makefile:108: core.aln] Error 255 #277

Closed spencer411 closed 3 years ago

spencer411 commented 3 years ago

Hi,

I am new to this software and had no problem downloading and running nullarbor.pl --check. It told me I deserve a medal! Nevertheless, when I try to run it with 6 test isolates I do not get a report folder in the OUTDIR. When I search the log for issues the only error I see is the following:

Use of uninitialized value in uc at /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/snippy-core line 392, line 1. Loaded 1 sequences totalling 0 bp. Illegal division by zero at /network/rit/lab/andamlab/bin/miniconda3/envs/nullarbor/bin/snippy-core line 145. make: *** [Makefile:108: core.aln] Error 255

Note that when I run it using "preview make", I do get the report folder, and it tells me the quality of all of my isolates is good.

Any idea what the issue is here? I have tried it with two different test sets, so I do not think it is an issue with the .fq files.

Any help is greatly appreciated.

spencer411 commented 3 years ago

So I did a clean install with conda, and it seems to be working better but still no report folder. The error seems to be related to snippy, but more specifically to samtools (from 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 5 --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

spencer411 commented 3 years ago

it was a memory issue, working it out.