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phac-nml / snvphyl-galaxy-cli

A command line interface for the SNVPhyl Galaxy pipeline.
Apache License 2.0
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running snvphyl by CLI produces an error #8

Open avpg3 opened 9 months ago

avpg3 commented 9 months ago

Dear contact, I am running the following SNVPhyl command (see below) and I get a random error that stops the workflow when is around ~80-87% complete. I am running the analysis for > 80 libraries and I haven't been able to complete the workflow; I suspect it has to do with resources allocated to the docker, but I don't know how to pass more resources for it to complete the whole process. Any help will be greatly appreciated!

command: bin/snvphyl.py --deploy-docker --min-coverage 5 --fastq-dir /fastqs/group_3a --reference-file ASM101963v1_genomic.fasta --output-dir ASM101963v1_output_group_3a --docker-cpus 72

Error: Waiting for workflow completion

percent complete (can initially decrease as more jobs are scheduled by Galaxy): 0...32.394366197183096...32.394366197183096...32.394366197183096...33.80281690140845...35.2112676056338...35.2112676056338...39.436619718309856...39.436619718309856...45.070422535211264...47.88732394366197...52.11267605633803...57.74647887323944...60.563380281690144...60.563380281690144...64.78873239436619...67.6056338028169...67.6056338028169...70.4225352112676...70.4225352112676...70.4225352112676...70.4225352112676...70.4225352112676...70.4225352112676...71.83098591549296...71.83098591549296...73.2394366197183...73.2394366197183...73.2394366197183...73.2394366197183...73.2394366197183...73.2394366197183...76.05633802816901...76.05633802816901...77.46478873239437...77.46478873239437...77.46478873239437...77.46478873239437...77.46478873239437...77.46478873239437...77.46478873239437...77.46478873239437...81.69014084507042...81.69014084507042...81.69014084507042...84.50704225352112...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182...87.32394366197182 Error occured while running workflow, downloading existing output files

Searching for dataset with name filterStats.txt Searching for dataset with name mappingQuality.txt Searching for dataset with name phylogeneticTree.newick Searching for dataset with name snvAlignment.phy Searching for dataset with name snvMatrix.tsv Exception occured when downloading snvMatrix.tsv, skipping... DatasetStateException("Dataset state is not 'ok'. Dataset id: fa6833a4eadf9064, current state: error"): Dataset state is not 'ok'. Dataset id: fa6833a4eadf9064, current state: error Searching for dataset with name snvTable.tsv Searching for dataset with name vcf2core.tsv

Writing Galaxy provenance info

Undeploying and cleaning up Docker Container

Running 'docker rm -f -v 227c86415953294e02b471ade660568fe8a452bc6dfbbb432185589312f027e5' 227c86415953294e02b471ade660568fe8a452bc6dfbbb432185589312f027e5 Traceback (most recent call last): File "bin/snvphyl.py", line 1302, in main(snvphyl_version_settings, **dic) File "bin/snvphyl.py", line 974, in main repeat_minimum_length, repeat_minimum_pid, filter_density_window, filter_density_threshold, invalid_positions_file, output_dir) File "bin/snvphyl.py", line 1193, in main_galaxy raise Exception('error occured in workflow, history=['+history_name+'], problematic datasets=["'+'"; "'.join(dataset_error_list)+'"]') Exception: error occured in workflow, history=[snvphyl-ASM101963v1_genomic-2024-01-17-run], problematic datasets=["snvMatrix.tsv"]

apetkau commented 9 months ago

Hello @avpg3 , try passing --keep-docker so that the Docker/Galaxy instance is not shutdown after failure. You can then login to the instance of Galaxy running with the following credentials:

From there you can take more detailed looks on what is causing issues (https://snvphyl.readthedocs.io/en/latest/user/usage/#managing-errors)