ERROR: could not find sequence of contig 'Y' about arriba

[suhrig]

This may either be a case of unexpected behavior on Mac, or your hg38.fa is really missing the Y chromosome (probably due to a corrupt download). Can you check, if the sequence is present:

grep chrY /Volumes/bam/DRG/annotations/hg38.fa

This should give you:

>chrY
>chrY_KI270740v1_random
>chrY_KZ208923v1_fix
>chrY_KZ208924v1_fix
>chrY_KN196487v1_fix

I just tested the FastA and GTF files you linked. Arriba does not throw the error on my system (Linux). I will test it on a Mac next. Hopefully, I will find some time tomorrow.

[chahatupreti]

It's pretty strange. I do have the Y chromosome -

| => grep chrY /Volumes/bam/DRG/annotations/hg38.fa
>chrY
>chrY_KI270740v1_random
>chrY_KZ208923v1_fix
>chrY_KZ208924v1_fix
>chrY_KN196487v1_fix

And yet it gives the error I mentioned! This is very mysterious.

[suhrig]

I was able to reproduce your problem on a Mac! Just as suspected the root cause is a Mac peculiarity. The function I use to check if a file is empty behaves differently on Mac than on Linux. Mac always reports the file as empty and therefore nothing gets read at all. Arriba only complains about chromosome Y, because that's the first one it checks, but really all of the chromosomes are missing.

Incidentally, I have already fixed the issue in my local code repository, because I recently made some optimizations to the routine that loads the assembly. This optimization happens to circumvent the Mac issue. I will push the changes to GitHub sooner or later. Until then, there is an easy workaround: You should only pass gzipped files to Arriba (i.e., whenever you use -a, -g, -b, -d, or -k). Loading of gzipped files uses different code, so there the issue is not triggered. BAM and SAM files (arguments -c and -x) need not be zipped, because they also use different code for loading.

[chahatupreti]

Hi Sebastian,

Your suggestion to use the gzipped file worked! Thanks a lot for the prompt and detailed response.