freyja issue?

[eraparroyo99]

reinstalled my wsl ubuntu from scratch reinstalled anaconda, python, docker, nextflow

result: N E X T F L O W ~ version 23.10.1 Launching CoPi/main.nf [sick_banach] DSL2 - revision: 9a59f5b6be executor > local (9) executor > local (9) executor > local (9) [ca/4007fc] process > concat (Concatenating fasta files into all_se... [100%] 1 of 1 ✔ [64/eb1e8c] process > pangolin (Lineage assignment using pangolin t... [ 0%] 0 of 1 [8f/993164] process > nextclade (Lineage assignment using nextclade) [ 0%] 0 of 1 [- ] process > lineage_assignment - [- ] process > bammix - [- ] process > bam_filter - [be/65ce08] process > virstrain (Identifying lineage assignment for... [ 0%] 0 of 3 [81/8598ea] process > freyja (Identifying relative lineage abundanc... [ 0%] 0 of 3 [- ] process > freyja_demix - [- ] process > freyja_aggregate - [- ] process > freyja_plot - [- ] process > makevcf - [- ] process > bammixplot - [- ] process > aafplot_mutations - [- ] process > aafplot_amplicons - [- ] process > ampliconsorting_DeltaReads - [- ] process > ampliconsorting_OmicronReads - [- ] process > ampliconsorting_samtools - [- ] process > ampliconsorting_bgzip - [- ] process > ampliconsorting_fasta - [- ] process > ampliconsorting_lineageAssignment_Pangolin - [- ] process > ampliconsorting_lineageAssignment_Nextclade - [- ] process > report - ERROR ~ Error executing process > 'freyja (Identifying relative lineage abundances of samples to see potential coinfection)'

Caused by: Process freyja (Identifying relative lineage abundances of samples to see potential coinfection) terminated with an error exit status (126)

Command executed:

freyja variants barcode08.bam --variants barcode08_variants.tsv --depths barcodeexecutor > local (9) [ca/4007fc] process > concat (Concatenating fasta files into all_se... [100%] 1 of 1 ✔ [64/eb1e8c] process > pangolin (Lineage assignment using pangolin t... [100%] 1 of 1, failed: 1 ✘ [8f/993164] process > nextclade (Lineage assignment using nextclade) [100%] 1 of 1, failed: 1 ✘ [- ] process > lineage_assignment - [- ] process > bammix - [- ] process > bam_filter - [be/65ce08] process > virstrain (Identifying lineage assignment for... [100%] 3 of 3, failed: 3 ✘ [10/6fd6f1] process > freyja (Identifying relative lineage abundanc... [100%] 2 of 2, failed: 2 [- ] process > freyja_demix - [- ] process > freyja_aggregate - [- ] process > freyja_plot - [- ] process > makevcf - [- ] process > bammixplot - [- ] process > aafplot_mutations - [- ] process > aafplot_amplicons - [- ] process > ampliconsorting_DeltaReads - [- ] process > ampliconsorting_OmicronReads - [- ] process > ampliconsorting_samtools - [- ] process > ampliconsorting_bgzip - [- ] process > ampliconsorting_fasta - [- ] process > ampliconsorting_lineageAssignment_Pangolin - [- ] process > ampliconsorting_lineageAssignment_Nextclade - [- ] process > report - ERROR ~ Error executing process > 'freyja (Identifying relative lineage abundances of samples to see potential coinfection)'

Caused by: Process freyja (Identifying relative lineage abundances of samples to see potential coinfection) terminated with an error exit status (126)

Command executed:

freyja variants barcode08.bam --variants barcode08_variants.tsv --depths barcode08_depth.tsv --ref /home/neil/CoPi/assets/sars-cov-2/reference-sequence.fasta

Command exit status: 126

Command output: (empty)

Command error: /etc/bash.bashrc: line 7: PS1: unbound variable docker: permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Head "http://%2Fvar%2Frun%2Fdocker.sock/_ping": dial unix /var/run/docker.sock: connect: permission denied. See 'docker run --help'.

Work dir: /home/neil/work/21/914b563ccb2c24c7710fcbcb6beb26

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details

[lanadelrea]

The docker is not online sir. Kindly check if docker is working or you can also use the conda option to run the pipeline. Thanks po!