Closed trum994 closed 1 year ago
Hi,
I will take longer to respond to issues as I am on paternity leave. This error comes from kaleido, which is a nice way to write the dynamic HTML plots into static PNGs. Unfortunately, it also leads to rather cryptic errors (especially on WSL, it seems). One way to solve this is that I have a try-except around calling kaleido, and this catches some errors without crashing NanoPlot. To "work around" other issues I recently added a --no_static option to skip the kaleido step, but that leaves you with only the HTML files and report. That probably is not a solution here?
So I understood that NanoPlot did not actually crash, but the expected png was not created?
Wouter
Thanks for the response Wouter. I think you are correct that nanoplot didn't actually crash. Exit status was zero, and the output contained the html reports. However nfcore nanoseq workflow expects the png files which were not created:
Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCBASECALL_PYCOQC_NANOPLOT:NANOPLOT (sample1)'
Caused by: Missing output file(s)
summary/*.png
expected by processNFCORE_NANOSEQ:NANOSEQ:QCBASECALL_PYCOQC_NANOPLOT:NANOPLOT (sample1)
So I either need to find a way to fix this kaleido problem or tell nanoseq workflow not to expect png plots. Let me know if you can think of a workaround. (and congrats on the little one!)
I'm running into this same error while running our SARS-CoV-2 pipeline with Nanopore data using NFCORE_VIRALRECON
during NFCORE_VIRALRECON:NANOPORE:NANOPLOT
Caused by:
Missing output file(s) `*.png` expected by process `NFCORE_VIRALRECON:NANOPORE:NANOPLOT (sample)`
Command executed:
NanoPlot \
\
-t 2 \
--fastq sample.fastq.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_VIRALRECON:NANOPORE:NANOPLOT":
nanoplot: $(echo $(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*$//')
END_VERSIONS
Command exit status:
0
Command output:
(empty)
@trum994 did you ever find a workaround for this?
Thanks!
I'm running into this problem when using the nfcore nanoseq workflow which calls nanoplot. How can I help debug?