Process `consensus_classification (5)` terminated with an error exit status (255)

[ysuzuki1978]

I am doing a bacterial flora analysis in nanopore and would like to use and look at this excellent tool, but I can't use it because of an error. Please let me know how to deal with this problem.

sudo nextflow run main.nf -profile test,docker

[d3/4d49ee] NOTE: Process consensus_classification (5) terminated with an error exit status (255) -- Execution is retried (1) [12/dfaec4] NOTE: Process consensus_classification (5) terminated with an error exit status (255) -- Execution is retried (2) [dc/529c30] NOTE: Process consensus_classification (5) terminated with an error exit status (255) -- Execution is retried (3) [e6/094006] NOTE: Process consensus_classification (5) terminated with an error exit status (255) -- Execution is retried (4) [bd/8e0428] NOTE: Process consensus_classification (5) terminated with an error exit status (255) -- Execution is retried (5) Error executing process > 'consensus_classification (5)'

Caused by: Process consensus_classification (5) 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/yakuri/nanopore/NanoCLUST/work/e1/71c8fae9dfac35efc380d320f67b33

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

[josiah-liew]

Hello @ysuzuki1978 you can try this solution that has been mentioned in a previous comment #70. This fixed exit status (255) for me. All the best!