pseudoalignments.tsv error

[Bondada20]

FileNotFoundError: [Errno 2] No such file or directory: '/tmp/arcas_e8c94069-a619-4cc1-b53c-789445ed2377/pseudoalignments.tsv'

[kalanir]

I'm also having this issue when running arcasHLA genotype

[IntelligentRock]

I have the same issue, also no such file or directory: pseudoaligments.tsv. Running arcasHLA genotype on fastq.gz files.

[ShihanL]

Looks like it's an issue with kallisto versions, must be 0.44.0. Newer versions appear to cause this bug

[IntelligentRock]

Looks like it's an issue with kallisto versions, must be 0.44.0. Newer versions appear to cause this bug

This doens't fix it for me. I still get the same error on 0.44.0. Did you change anything else? The actual file its looking for, pseudocount.tsv, also doesn't exist in the folder, only trim.reads.txt.

[asaksager]

I also have this problem, and I cannot use kallisto 0.44.0 (0.51.0 instead) as it is not avaible.
Did you find a solution?
@IntelligentRock @ShihanL @kalanir @andreas-wilm

[IntelligentRock]

I also have this problem, and I cannot use kallisto 0.44.0 (0.51.0 instead) as it is not avaible. Did you find a solution? @IntelligentRock @ShihanL @kalanir @andreas-wilm

No. Even with Kallisto 0.44.0 it won't work, I also encountered a lot of other issues with arcas, so I decided to use nf-core/hlatyping. I recommend trying it out to see if it meets your requirements.

[BERICP01]

Same issue!

[vivianschu]

I also have this same issue!

[Ryan-3]

I think this just happens if Kallisto fails in general. For me, it was because I missed arcasHLA genotype also required --single to indicate single-end reads. That error was in the log. Once I fixed that, it worked.