Difficulty in running Mmseqs2 and the others after the Roary results

[Ekuufire-30]

nextflow run hoelzer-lab/ribap -r 1.0.0 --fasta "/home/emma/campy/project_campy/sequences/fasta/*fasta"

Please after changing to the above command on conda to suit my profile. I am not still able to run the program on for my genomes. I would be grateful if you could assist in this regard. Really need this to finish up my project.

I keep getting the error message below. Thanks

ERROR ~ Error executing process > 'RIBAP:mmseqs2'

Caused by: Process RIBAP:mmseqs2 terminated with an error exit status (127)

Command executed:

mkdir mmseq2 cat *.faa > mmseq2/all_proteins.fa MMSEQDB="mmseq2/mmseq2.db"

Creating DB

mmseqs createdb mmseq2/all_proteins.fa $MMSEQDB

Creating Index

mmseqs createindex --threads 4 $MMSEQDB mmseq2/tmp

Starting MMSeqs2 Search

mmseqs search --threads 4 $MMSEQDB $MMSEQDB "${MMSEQDB%.*}_result" mmseq2/tmp -a

Converting results

mmseqs convertalis --format-output "query,target,pident,alnlen,mismatch,gapopen,qstart,qend,qlen,tstart,tend,tlen,qcov,tcov,evalue,bits" --threads 4 $MMSEQDB $MMSEQDB "${MMSEQDB%.}_result" "${MMSEQDB%.}_result.csv"

cat "${MMSEQDB%.}_result.csv" | awk '{if($3>0.6 && $13>0.4){print $0}}' > "${MMSEQDB%.}_result_filtered.csv"

mv mmseq2/mmseq2_result.csv . mv mmseq2/mmseq2_result_filtered.csv .

Command exit status: 127

Command output: (empty)

Command error: .command.sh: line 7: mmseqs: command not found

Work dir: /home/emma/campy/project_campy/sequences/fasta/work/cc/447c10355d60b401a08a80509c8266

[hoelzer]

Hey @Ekuufire-30

It seems that mmseqs2 is not installed which should either happen via conda or docker/singularity depending on your setup and the used -profile.

Also you could try the latest release version. And use single tick symbols to input multiple files! Otherwise nextflow will only read the first FASTA. Please also read the manual carefully before starting the pipeline.

Then, you can try:

nextflow pull hoelzer-lab/ribap
nextflow run hoelzer-lab/ribap -r 1.0.3 --fasta '/home/emma/campy/project_campy/sequences/fasta/*fasta' -profile local,conda

However, I recommend docker instead of conda, if that is possible for you. It seems you are running the pipeline on a local machine? A laptop or workstation? If so, you might have the permission to install Docker. However, you can also first try via -profile local,conda as suggested above.

[Ekuufire-30]

Hello @hoelzer Your recommendations did the magic! I am so grateful for the assistance. I used the latest version of ribap and install all the other requirements and boom it worked. Thanks, Emmanuel

[hoelzer]

Great! Glad to hear. Please also check our recent paper in Genome Biology for further details (and limitations) of RIBAP.

Cheers, Martin