Issue about initiating diamond

[jlk666]

Dear authors I have a question when I try running

emapper.py -m diamond -i GCF_000196095.1_ASM19609v1_translated_cds.faa --itype CDS -o a1 /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond blastx -d /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnog-mapper-data/eggnog_proteins.dmnd -q /Users/jlk666/Documents/Project/Vibrio_project/annotation/GCF_000196095.1_ASM19609v1_translated_cds.faa --threads 1 -o /Users/jlk666/Documents/Project/Vibrio_project/annotation/test.emapper.hits --sensitive -e 0.001 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp Error running diamond: /bin/sh: /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond: cannot execute binary file It always shows that

I have downloaded all required database and software

[Cantalapiedra]

Hi @jlk666 ,

You could try running the diamond command directly to check the error:

/Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond blastx -d /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnog-mapper-data/eggnog_proteins.dmnd -q /Users/jlk666/Documents/Project/Vibrio_project/annotation/GCF_000196095.1_ASM19609v1_translated_cds.faa --threads 1 -o /Users/jlk666/Documents/Project/Vibrio_project/annotation/test.emapper.hits --sensitive -e 0.001 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp

I am not sure if the diamond bundled along with eggnog-mapper will be valid for your OS. You may need to install a diamond which runs in your system.

Best, Carlos

[jlk666]

Hi Carlos I appreciate your quick response! When I run the code you provided it appears this. I try running eggNOG in my macOS terminal.

zsh: exec format error: /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond

[Cantalapiedra]

Hi @jlk666 ,

glad to try to help. I don't have macOS myself. Maybe you should try to install a diamond version for macOS, and add it to the path, so that eggnog-mapper can use that one instead of the bundled one.

Best, Carlos

[jlk666]

Thank you for your greatly helpful advice! I have downloaded the correct diamond for MacOS However, when I run

jlk666@campus-107-177 annotation % emapper.py -m diamond -i GCF_000196095.1_ASM19609v1_translated_cds.faa --itype CDS -o ip

emapper-2.1.1-1

emapper.py -m diamond -i GCF_000196095.1_ASM19609v1_translated_cds.faa --itype CDS -o ip

/Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond blastx -d /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnog-mapper-data/eggnog_proteins.dmnd -q /Users/jlk666/Documents/Project/Vibrio_project/annotation/GCF_000196095.1_ASM19609v1_translated_cds.faa --threads 1 -o /Users/jlk666/Documents/Project/Vibrio_project/annotation/ip.emapper.hits --sensitive -e 0.001 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp Error running diamond: Error: Invalid output field: scovhsp

and even jlk666@campus-107-177 annotation % /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/diamond blastx -d /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnog-mapper-data/eggnog_proteins.dmnd -q /Users/jlk666/Documents/Project/Vibrio_project/annotation/GCF_000196095.1_ASM19609v1_translated_cds.faa --threads 1 -o /Users/jlk666/Documents/Project/Vibrio_project/annotation/test.emapper.hits --sensitive -e 0.001 --top 3 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp scovhsp

diamond v0.9.14.115 | by Benjamin Buchfink buchfink@gmail.com Licensed under the GNU AGPL https://www.gnu.org/licenses/agpl.txt Check http://github.com/bbuchfink/diamond for updates.

CPU threads: 1

Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Error: Invalid output field: scovhsp

Maybe something run about the output?

[Cantalapiedra]

Hi @jlk666 ,

it's weird that it is using diamond 0.9. What is the output of emapper.py --version? And what is the content of /Users/jlk666/Documents/Project/Vibrio_project/annotation/eggnog-mapper/eggnogmapper/bin/ directory?

[jlk666]

(base) jlk666@campus-107-177 annotation % emapper.py --version emapper-2.1.1-1

(base) jlk666@campus-107-177 bin % ls init.py esl-mask hmmlogo alimask esl-reformat hmmpgmd diamond esl-selectn hmmpress diamond_0.9.24 esl-seqrange hmmscan diamond_2.0.4 esl-seqstat hmmsearch esl-afetch esl-sfetch hmmsim esl-alimanip esl-shuffle hmmstat esl-alimap esl-ssdraw jackhmmer esl-alimask esl-stranslate makehmmerdb esl-alimerge esl-weight mmseqs esl-alipid hmmalign nhmmer esl-alistat hmmbuild nhmmscan esl-cluster hmmc2 phmmer esl-compalign hmmconvert prodigal esl-compstruct hmmemit prodigal.linux esl-construct hmmerfm-exactmatch esl-histplot hmmfetch

[Cantalapiedra]

Hi @jlk666 ,

I really don't know why in your system it is running diamond 0.9. You may need to install diamond 2.0.4 instead.

https://github.com/bbuchfink/diamond/releases/tag/v2.0.4

[jlk666]

Thank you so much. Based on your suggestion, I have successfully run eggNOG in my macOS. Many thanks!

[Cantalapiedra]

Glad that you finally made it. Sorry for not being very helpful with macOS, and thank you for your patience.

Best, Carlos