Warning raised : unknown recognition error type

[tamuanand]

Hi @pditommaso

This is with reference to the slack message - https://nextflow.slack.com/archives/C02T98A23U7/p1645882378629219?thread_ts=1645831697.830129&cid=C02T98A23U7

This warning pops up

unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

When do I see this:

• lets say I have 2 terminal windows
• I launch a NF job with awsbatch executor on Terminal 1 - this does Not trigger the warning
• When I now launch a NF job with awsbatch executor on Terminal 2 - the warning shows up.

As mentioned by Sateesh Peri, the job runs fine and produces the necessary results.

Environment

• Nextflow version: 21.12.1.edge
• Java version: openjdk version "1.8.0_312"
• Operating system: Amazon Linux 2
• Bash version: GNU bash, version 4.2.46(2)-release (x86_64-koji-linux-gnu)

[sateeshperi]

hi @pditommaso here is a gitpod to replicate my setup. nextflow run main.nf -profile docker,test after launch and you will see the error after configs are printed to terminal

[pditommaso]

This looks like something weird in the pipeline code, but it's not accessible

https://github.com/nf-core/mycosnp/

[sateeshperi]

@pditommaso here is the link to repo https://github.com/CDCgov/mycosnp-nf

[pditommaso]

To look into this, it's required minimal testing that replicate the problem. This pipeline it's too big for a troubleshooting

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[BrunoGrandePhD]

For others who stumble upon this issue, I was able to solve it by removing a stray \ in my process script (i.e. the one before --ncbi-build):

vcf2maf.pl \
    --input-vcf ${input_vcf} --output-maf output.maf --ref-fasta ${reference_fasta} \
    --vep-data ${vep_data} \--ncbi-build GRCh38 --max-subpop-af 0.0005 \
    --maf-center "Sage Bionetworks"

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.