"Searching alignments... Failed to run diamond." then (from diamond)"Searching alignments... Illegal instruction: 4" about carveme

[cdanielmachado]

Which version of diamond is installed?

Some users have experienced problems with diamond 0.9. If you have it, please downgrade to the latest release of diamond 0.8.

Let me know if this works.

[jbholm]

Thank you - I was using 0.9. I downgraded, uninstalled and reinstalled carveme and it is working now.

[jbholm]

I now get this error:

Failed to parse: tig00003672_IGS_ANNOTATED_Editted_-_V-type_H(+)-translocating_pyrophosphatase_CDS

Is this because of unacceptable characters in the header?

[cdanielmachado]

Can you copy the complete error message? I am not sure if the error is coming from diamond or carveme...

[jbholm]

carve tig00003672_IGS_ANNOTATED_Editted.faa -v
Running diamond...
diamond blastp -d /miniconda2/lib/python2.7/site-packages/carveme/data/input/bigg_proteins.dmnd -q tig00003672_IGS_ANNOTATED_Editted.faa -o tig00003672_IGS_ANNOTATED_Editted.tsv --more-sensitive --top 10
Loading universe model...
Scoring reactions...
Reconstructing a single model
Failed to parse: tig00003672_IGS_ANNOTATED_Editted_-_V-type_H(+)-translocating_pyrophosphatase_CDS
Done.

It produced output files - I'm just not sure what happened with this one protein.

From the output - what visualizer do you recommend? Is there a source containing the column headers for output tsv file?

[cdanielmachado]

Sorry, I just realized i forgot to reply to this message. The problem here is that tig00003672_IGS_ANNOTATED_Editted_-_V-type_H(+)-translocating_pyrophosphatase_CDS is not a valid gene identifier. But the problem originates with the fasta file.