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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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"Searching alignments... Failed to run diamond." then (from diamond)"Searching alignments... Illegal instruction: 4" #58

Closed jbholm closed 3 years ago

jbholm commented 4 years ago

Hi, I'm trying to run carve but initially hit the error: "Searching alignments... Failed to run diamond."

I then ran the specific diamond command: diamond blastp -d /miniconda2/lib/python2.7/site-packages/carveme/data/input/bigg_proteins.dmnd -q PROKKA_08182019.faa -o PROKKA_08182019.tsv --more-sensitive --top 10

which resulted in the following error: Searching alignments... Illegal instruction: 4

Thus, I know diamond is being found properly by carve. But something is happening within diamond to prevent alignment search.

Any help is appreciated - thanks!

p.s. I am attempting to run on this on macOSX - thus using the macOSX diamond installed using conda**

cdanielmachado commented 4 years ago

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 commented 4 years ago

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

jbholm commented 4 years ago

I now get this error:

Failed to parse: tig00003672_IGS_ANNOTATEDEditted-_V-type_H(+)-translocating_pyrophosphatase_CDS

Is this because of unacceptable characters in the header?

cdanielmachado commented 4 years ago

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

jbholm commented 4 years ago

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_ANNOTATEDEditted-_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 commented 3 years ago

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.