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genepi / mtdna-server-2

mtDNA-Server 2: A web-service and Nextflow pipeline for mitochondrial genomes
MIT License
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no-home option error #20

Closed fmurgia closed 4 months ago

fmurgia commented 5 months ago

HI, I ran the pipeline in my server (nextflow run genepi/mtdna-server-2 -r v2.1.9 -profile test,singularity) using your test dataset and I get this error: "ERROR: Unknown option: --no-home"

Can you help with this?

nextflow run genepi/mtdna-server-2 -r v2.1.9 -profile test,singularity Nextflow 24.04.1 is available - Please consider updating your version to it N E X T F L O W ~ version 23.10.1 Launching https://github.com/genepi/mtdna-server-2 [irreverent_jepsen] DSL2 - revision: 1140d5c7fd [v2.1.9] Welcome to mtDNA-Server 2 v2.1.9 (c) Sebastian Schönherr, Hansi Weissensteiner, Lukas Forer WARN: Access to undefined parameter output_reports -- Initialise it to a default value eg. params.output_reports = some_value executor > local (2) [be/5d16b1] process > MTDNA_SERVER_2:INDEX [100%] 1 of 1, failed: 1 ✘ [20/03d34c] process > MTDNA_SERVER_2:CALCULATE_STATISTICS (1) [100%] 1 of 1, failed: 1 ✘ [- ] process > MTDNA_SERVER_2:INPUT_VALIDATION - [- ] process > MTDNA_SERVER_2:QUALITY_CONTROL - [- ] process > MTDNA_SERVER_2:MUTSERVE - [- ] process > MTDNA_SERVER_2:MUTECT2 - [- ] process > MTDNA_SERVER_2:FILTER_VARIANTS - [- ] process > MTDNA_SERVER_2:MERGING_VARIANTS - [- ] process > MTDNA_SERVER_2:VCF_MERGE - [- ] process > MTDNA_SERVER_2:HAPLOGROUPS_CONTAMINATION - [- ] process > MTDNA_SERVER_2:COVERAGE_ESTIMATION - [- ] process > MTDNA_SERVER_2:ANNOTATE - [- ] process > MTDNA_SERVER_2:REPORT - [- ] process > MTDNA_SERVER_2:SAMPLE_REPORT - ERROR ~ Error executing process > 'MTDNA_SERVER_2:INDEX'

Caused by: Process MTDNA_SERVER_2:INDEX terminated with an error exit status (1)

Command executed:

samtools faidx mt_contigs.fasta samtools dict mt_contigs.fasta -o mt_contigs.dict

Command exit status: 1

Command output:

Command error: ERROR: Unknown option: --no-home

seppinho commented 5 months ago

Thanks. I was able to execute it on singularity without errors. Can you copy/paste the error message from the work directory (work/be/5d16b1/.command.log or .command.err). I believe it could be a singularity problem (--no-home is an option we're not setting in the code). My server runs singularity version 3.8.3. You could also try to run it with Docker if possible.

fmurgia commented 5 months ago

HI,

here are the log files:

.command.log:

ERROR: Unknown option: --no-home (B

command.err:

ERROR: Unknown option: --no-home

Also, command.run command.run.txt

I hope they can help.

seppinho commented 5 months ago

interesting but again I think this is a singularity problem not a pipeline profile. You could also try with the latest version v2.1.13 but I think this is not related to the pipeline