You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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 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?
The text was updated successfully, but these errors were encountered:
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
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?
The text was updated successfully, but these errors were encountered: