Error running test

[claudiodonati]

Hi, I tried to run the test

nextflow run main.nf -profile test,docker

and I got the following error:

Error executing process > 'consensus_classification (1)'

Caused by: Process consensus_classification (1) terminated with an error exit status (255)

Command executed:

export BLASTDB= export BLASTDB=$BLASTDB:/tmp/db/taxdb/ blastn -query consensus.fasta -db /tmp/db/16S_ribosomal_RNA -task blastn -dust no -outfmt "10 sscinames staxids evalue length pident" -evalue 11 -max_hsps 50 -max_target_seqs 5 | sed 's/,/;/g' > consensus_classification.csv

DECIDE FINAL CLASSIFFICATION

cat 0_draft.log > 0_blast.log echo -n ";" >> 0_blast.log BLAST_OUT=$(cut -d";" -f1,2,4,5 consensus_classification.csv | head -n1) echo $BLAST_OUT >> 0_blast.log

Command exit status: 255

Command output: (empty)

Command error: Error: NCBI C++ Exception: T0 "/opt/conda/conda-bld/blast_1595737360567/work/blast/c++/src/serial/objistrasnb.cpp", line 499: Error: (CSerialException::eOverflow) byte 95: overflow error ( at [].[].gi) T0 "/opt/conda/conda-bld/blast_1595737360567/work/blast/c++/src/serial/member.cpp", line 768: Error: (CSerialException::eOverflow) ncbi::CMemberInfoFunctions::ReadWithSetFlagMember() - error while reading seqid ( at Blast-def-line-set.[].[].seqid.[].[].gi)

Work dir: /home/donatic/Downloads/NanoCLUST-master/work/6e/1e99805a8a3bdd0234ae3ae5dfb9ff

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

[nf-core/nanoclust] Pipeline completed with errors

Any hint?

[poursalavati]

As reported by other users, this problem is caused by the incompatibility of the blast version with the updated NCBI databases. After repeated changes and tests, now the best way to bypass the problem in docker mode is to edit the following file like this (change the old blast to the new version):

nextflow.config

line 104: withName: consensus_classification { container = 'ncbi/blast:latest'

Best, NP

[claudiodonati]

Now it works. Thanks a lot

[ccuriqueo]

Thank you so much!!, now it finished without errors