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I am using pATLASflow to detect the plasmids in my assembled contig sequence. I downloaded the nexflow using this command wget -qO- https://get.nextflow.io | bash, made its executable using chmod and then using the following command to detect the available plasmids ./nextflow run tiagofilipe12/pATLASflow --assembly --fasta "path to the fasta file of the assembled contig". However, after running the above command, I am receiving the following output:
"
N E X T F L O W ~ version 21.10.4
Launching tiagofilipe12/pATLASflow [extravagant_descartes] - revision: 7cec748 [master]
executor > local (1)
[- ] process > mashScreen -
[- ] process > mashOutputJson -
[d0/178da8] process > runMashDist (running mash dist for fasta file: 562.22835.fasta) [100%] 1 of 1, failed: 1 ✘
[- ] process > mashDistOutputJson -
[- ] process > mappingBowtie -
[- ] process > samtoolsView -
[- ] process > jsonDumpingMapping -
[- ] process > fullConsensus -
Error executing process > 'runMashDist (running mash dist for fasta file: 562.22835.fasta)'
Caused by:
Process runMashDist (running mash dist for fasta file: 562.22835.fasta) terminated with an error exit status (1)
Hi,
I am using pATLASflow to detect the plasmids in my assembled contig sequence. I downloaded the nexflow using this command
wget -qO- https://get.nextflow.io | bash
, made its executable using chmod and then using the following command to detect the available plasmids./nextflow run tiagofilipe12/pATLASflow --assembly --fasta "path to the fasta file of the assembled contig"
. However, after running the above command, I am receiving the following output:"
N E X T F L O W ~ version 21.10.4
Launching tiagofilipe12/pATLASflow [extravagant_descartes] - revision: 7cec748 [master]
executor > local (1)
[- ] process > mashScreen -
[- ] process > mashOutputJson -
[d0/178da8] process > runMashDist (running mash dist for fasta file: 562.22835.fasta) [100%] 1 of 1, failed: 1 ✘
[- ] process > mashDistOutputJson -
[- ] process > mappingBowtie -
[- ] process > samtoolsView -
[- ] process > jsonDumpingMapping -
[- ] process > fullConsensus -
Error executing process > 'runMashDist (running mash dist for fasta file: 562.22835.fasta)'
Caused by:
Process
runMashDist (running mash dist for fasta file: 562.22835.fasta)
terminated with an error exit status (1)Command executed:
mash dist -i -p 1 -v 0.05 -d 0.1 /ngstools/data/plasmid_db_reference.msh 562.22835.fasta > 562.22835.fasta_mashdist.txt
Command exit status:
1
Command output:
(empty)
Command wrapper:
.command.run: line 112: PYTHONPATH: unbound variable
"
I am not sure what I am doing wrong here.
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