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theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
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[Theiaproke_illumina_pe workflow: shovill_pe error] #538

Open wittawin-w opened 4 months ago

wittawin-w commented 4 months ago

:bug:

Hello, I ran the theiaproke workflow on my local computer (macOS, M3) using miniwdl. I faced with the aborting workflow when running task: shovill_pe. the run command is miniwdl run $HOME/tools/public_health_bioinformatics/workflows/theiaprok/wf_theiaprok_illumina_pe.wdl --input $HOME/Working_directory/Theiaprok_AFI_16s/input.json my input json file contains {samplename, read1, read2} after running the workflow trew the error message below: 2024-07-10 22:38:00.482 wdl.w:theiaprok_illumina_pe.t:call-shovill_pe output path not found in container (error unless declared type is optional) :: output: "assembly_fasta", path: "out/PC_S19_contigs.fasta" 2024-07-10 22:38:00.485 wdl.w:theiaprok_illumina_pe.t:call-shovill_pe task shovill_pe (../../tasks/assembly/task_shovill.wdl Ln 3 Col 1) failed :: dir: "/Users/wittawin/Working_directory/Theiaprok_AFI_16s/20240710_221721_theiaprok_illumina_pe/call-shovill_pe", error: "OutputError", message: "File/Directory path not found in task output assembly_fasta", node: "decl-assembly_fasta" 2024-07-10 22:38:00.489 wdl.w:theiaprok_illumina_pe call failure propagating :: from: "call-shovill_pe", dir: "/Users/wittawin/Working_directory/Theiaprok_AFI_16s/20240710_221721_theiaprok_illumina_pe" 2024-07-10 22:38:00.489 wdl.w:theiaprok_illumina_pe aborting workflow 2024-07-10 22:38:00.490 miniwdl-run File/Directory path not found in task output assembly_fasta :: error: "OutputError", node: "decl-assembly_fasta", dir: "/Users/wittawin/Working_directory/Theia prok_AFI_16s/20240710_221721_theiaprok_illumina_pe", from_dir: "/Users/wittawin/Working_directory/Theiaprok_AFI_16s/20240710_221721_theiaprok_illumina_pe/call-shovill_pe"

Here are error.json files error.json shovill_error.json How do I solve this problem.

Thank you

sage-wright commented 4 months ago

Hi!

Could you please send the stderr.txt and stdout.txt that was generated for the Shovill task? You can find it within the call-shovill_pe directory. If that's not available, could you send us the task.log file?

Once we get that information, I can help you figure out what's going on!

wittawin-w commented 4 months ago

shovill_stdout.txt shovill_stderr.txt

Thank you for your response. Here is the stdout.txt and stderr.txt of shovill for your consideration

sage-wright commented 4 months ago

Thank you! After looking at this, it looks like a fairly low number of reads were "merged/combined" by FLASH. Can you tell me more about your raw data (file size, number of raw and clean reads, etc) and the kraken2 outputs (raw and clean) to see if which taxon it belongs to?

If you are comfortable sharing your raw data, we can perform this and more investigation to figure out what has happened without additional back-and-forth! Whatever works for you.