A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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No default Qt backend for graphics when using -profile conda #59
When running the workflow with the option "-profile conda", the environment set up using environments/extras.yml does not have a graphics backend dependency included. On naive systems with no system-wide Qt library installed, this leads to a failure of qc.py and stops the workflow. Adding a libxcb entry to the extras.yml file solves this issue (pull request provided).
Command error:
qt.qpa.plugin: Could not find the Qt platform plugin "xcb" in ""
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
When running the workflow with the option "-profile conda", the environment set up using environments/extras.yml does not have a graphics backend dependency included. On naive systems with no system-wide Qt library installed, this leads to a failure of qc.py and stops the workflow. Adding a libxcb entry to the extras.yml file solves this issue (pull request provided).
WARN: Killing pending tasks (34) Error executing process > 'ncovIllumina:sequenceAnalysis:makeQCCSV (Li18584_S333_L002)'
Caused by: Process
ncovIllumina:sequenceAnalysis:makeQCCSV (Li18584_S333_L002)terminated with an error exit status (134)Command executed:
qc.py --illumina --outfile AB_ARTIC_v3_Illumina_run1_plates_2_3_4_5_novaseq.Li18584_S333_L002.qc.csv --sample Li18584_S333_L002 --ref ref.fa --bam Li18584_S333_L002.mapped.primertrimmed.sorted.bam --fasta Li18584_S333_L002.primertrimmed.consensus.fa
Command exit status: 134
Command output: (empty)
Command error: qt.qpa.plugin: Could not find the Qt platform plugin "xcb" in "" This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.
.command.sh: line 2: 7129 Aborted (core dumped) qc.py --illumina --outfile AB_ARTIC_v3_Illumina_run1_plates_2_3_4_5_novaseq.Li18584_S333_L002.qc.csv --sample Li18584_S333_L002 --ref ref.fa --bam Li18584_S333_L002.mapped.primertrimmed.sorted.bam --fasta Li18584_S333_L002.primertrimmed.consensus.fa
Work dir: /tiered/chgi_data/analysis/secondary/novaseq6000/200630_A00906_0051_AHMVWNDRXX/ncov2019-artic-nf/work/55/dc50d7c9a0e3402441a64b740f85b5
Tip: view the complete command output by changing to the process work dir and entering the command
cat .command.out