Process consensus_classification terminated with an error exit status (255)
fairquestion opened this issue · 4 comments
Dear all (is someone still maintaining this?),
I get this error when running the pipeline on just 1 .fastq file following exactly the instructions provided here, and yes, the test worked fine.
Guys, the idea of containerizing pipelines + pipeline managers is to avoid these kind of problems. NanoClust should run smooth, what is going on here? I am not the first one reporting this error: https://githubhot.com/repo/genomicsITER/NanoCLUST/issues/60
Command line used: nextflow run main.nf --reads "data/mydata.fastq" --db "db/16S_ribosomal_RNA" --tax "db/taxdb/" --max_memory "36.GB" --max_cpus 16 --max_time '2.h' -profile docker
Error:
Error executing process > 'consensus_classification (14)'
Caused by:
Process consensus_classification (14) terminated with an error exit status (255)
Command executed:
export BLASTDB=
export BLASTDB=$BLASTDB:/tmp/db/taxdb/
blastn -query consensus.fasta -db /tmp/db/16S_ribosomal_RNA -task blastn -dust no -outfmt "10 sscinames staxids evalue length pident" -evalue 11 -max_hsps 50 -max_target_seqs 5 | sed 's/,/;/g' > consensus_classification.csv
#DECIDE FINAL CLASSIFFICATION
cat 49_draft.log > 49_blast.log
echo -n ";" >> 49_blast.log
BLAST_OUT=$(cut -d";" -f1,2,4,5 consensus_classification.csv | head -n1)
echo $BLAST_OUT >> 49_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 98: 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)
see the post here for a solution:
https://githubhot.com/repo/genomicsITER/NanoCLUST/issues/43?page=1
I was trying the suggested solution. However, the run still failed with a different error. Now it was not able to find the blast directory. @fairquestion did you find a solution that worked until now?
honestly I gave up on this and moved to Emu. sorry I can't be of more help
I tried to write the db and taxdb paths without starting with the "/" character and I was able to pass the consensus classification. But I miss an error in the next step again. I do not know if related to the solution of the above.
Ex: nextflow run main.nf --reads "data/*.fastq" --db "db/16S_ribosomal_RNA" --tax "db/taxdb" -profile docker
The problem I think lies in the paths that NanoCLUST generates according to the different environments (computers of each person), files, ways to specify the routes ... It is a code that has to be customized according to the computer and how to run it.