SPAdes cp: cannot create regular file

[Siddra2021]

Describe the bug Pipeline runs successfully but no output is produced Impact No output generated

To Reproduce Steps to reproduce the behavior:

• What environment you are running the pipeline in (local
• What version of the pipeline you are using 1.0.0
• The command that was run to cause the error
• nextflow run cdcgov/phoenix -r v1.0.0 -profile docker -entry PHOENIX --input ~/phoenix/samplesheet.csv --kraken2db ~/phoenix/assets/databases/
• If you used a custom config file please provide it
• The text of the error itself - screenshots are great for this!
• Attached

Expected behavior should run successfully

Screenshots IAttached

[jvhagey]

Hi @Siddra2021, can you provide the .command.out and .command.err files for that spades step? We need to know why spades is failing.

[Siddra2021]

.command.err.txt .command.out.txt

[jvhagey]

@Siddra2021 it seems these are not specific to the SPAdes step, these are for the multiQC step. you need to follow the path to the spades specific step (in your case this is ef/dcBcc3).

[Siddra2021]

Attached .command.err.txt .command.out.txt

[jvhagey]

@Siddra2021 this is the same issue as #82 please read my responses there.