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Erro na rodada teste #35

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kayobianco opened this issue Oct 24, 2023 · 1 comment
Closed

Erro na rodada teste #35

kayobianco opened this issue Oct 24, 2023 · 1 comment

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@kayobianco
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Pessoal, tudo bem?

Instalei o Viralflow e estou tentando rodar o teste, mas sem sucesso. Segue o log:

(viralflow) kayobianco@:~/ViralFlow$ viralflow -run --params_file test_files/sars-cov-2.params
ViralFlow v0.1.0
NXF_VER=22.04.0 nextflow run /home/kayobianco/ViralFlow//vfnext/main.nf --virus sars-cov2 --outDir /home/kayobianco/ViralFlow/test_files/sars-cov-2/outputs --inDir /home/kayobianco/ViralFlow/test_files/sars-cov-2/input --runSnpEff true --writeMappedReads true --minLen 75 --depth 25 --minDpIntrahost 100 --trimLen 0 --fastp_threads 1 --bwa_threads 1 --mafft_threads 1 -resume
N E X T F L O W ~ version 22.04.0
Launching /home/kayobianco/ViralFlow/vfnext/main.nf [deadly_noether] DSL2 - revision: 72092b7946

===========================================
VFNEXT v0.1.0
parameters:

--inDir : /home/kayobianco/ViralFlow/test_files/sars-cov-2/input
--outDir : /home/kayobianco/ViralFlow/test_files/sars-cov-2/outputs
--virus : sars-cov2
--refGenomeCode *: null
--referenceGenome *: null
--referenceGFF *: null
--primersBED : null
--minLen : 75
--depth : 25
--minDpIntrahost : 100
--trimLen : 0
--databaseDir : /home/kayobianco/ViralFlow/vfnext/databases/
--runSnpEff : true
--writeMappedReads : true
--nextflowSimCalls : null
--fastp_threads : 1
--bwa_threads : 1
--mafft_threads : 1
--mapping_quality : 30
--base_quality : 30
--minBamSize : 500

  • Only required for "custom" virus
    Runtime data:

Running with profile: standard
Run container: [:]
Running as user: kayobianco
Launch dir: /home/kayobianco/ViralFlow
Base dir: /home/kayobianco/ViralFlow/vfnext

WARN: An BED file with primer positions was not provided. The pipeline will not run samtools clip to remove primer regions
WARN: Number of requested simultaneous nextflow calls (null) was set to max cpus available (8)
executor > local (4)
[ee/d272fc] process > processInputs:prepareDatabase [ 0%] 0 of 1
[- ] process > indexReferenceBWA -
[- ] process > genFaIdx -
[17/280151] process > runFastp (3) [ 0%] 0 of 3
[- ] process > align2ref -
[- ] process > getMappedReads -
[- ] process > getUnmappedReads -
[- ] process > bamToFastq -
[- ] process > runIvar -
[- ] process > runReadCounts -
[f9/ac819c] process > checkSnpEffDB [100%] 1 of 1, cached: 1 ✔
[- ] process > runSnpEff -
[- ] process > runVfReport -
[- ] process > alignConsensus2Ref -
[- ] process > runPicard -
[- ] process > fixWGS -
[- ] process > runIntraHostScript -
[- ] process > runPangolin -
[- ] process > runNextClade -
[- ] process > compileOutputs_SC2 -
Error executing process > 'processInputs:prepareDatabase'

Caused by:
Process processInputs:prepareDatabase terminated with an error exit status (127)

Command executed:

download fasta from NCBI

esearch -db nucleotide -query NC_045512.2 | efetch -format fasta > NC_045512.2.fa

download gff from NCBI

wget -O NC_045512.2.gff "https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&report=gff3&id=NC_045512.2"

Command exit status:
127
executor > local (4)
[ee/d272fc] process > processInputs:prepareDatabase [100%] 1 of 1, failed: 1 ✘
[- ] process > indexReferenceBWA -
[- ] process > genFaIdx -
[- ] process > runFastp (3) -
[- ] process > align2ref -
[- ] process > getMappedReads -
[- ] process > getUnmappedReads -
[- ] process > bamToFastq -
[- ] process > runIvar -
[- ] process > runReadCounts -
[f9/ac819c] process > checkSnpEffDB [100%] 1 of 1, cached: 1 ✔
[- ] process > runSnpEff -
[- ] process > runVfReport -
[- ] process > alignConsensus2Ref -
[- ] process > runPicard -
[- ] process > fixWGS -
[- ] process > runIntraHostScript -
[- ] process > runPangolin -
[- ] process > runNextClade -
[- ] process > compileOutputs_SC2 -
Error executing process > 'processInputs:prepareDatabase'

Caused by:
Process processInputs:prepareDatabase terminated with an error exit status (127)

Command executed:

download fasta from NCBI

esearch -db nucleotide -query NC_045512.2 | efetch -format fasta > NC_045512.2.fa

download gff from NCBI

wget -O NC_045512.2.gff "https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?db=nuccore&report=gff3&id=NC_045512.2"

Command exit status:
127

Command output:
(empty)

Command error:
WARNING: Skipping mount /etc/localtime [binds]: /etc/localtime doesn't exist in container
.command.sh: line 3: esearch: command not found
.command.sh: line 3: efetch: command not found

Work dir:
/home/kayobianco/ViralFlow/work/ee/d272fc7347ea6d851d97e45a2267ea

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

Podem ajudar?

@kayobianco kayobianco changed the title Errona rodada teste Erro na rodada teste Oct 24, 2023
@costahud
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Thanks for reporting this error, @kayobianco. The fix was provided (#40) and was solved on version 1.0.0.

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