Open gzentner opened 1 year ago
A user is seeing the same issue. How were you able to see the exact commands executed? I had to go into the work directory, listed at the end, and look at command.sh
:
$ more .command.sh
#!/bin/bash -euo pipefail
NanoPlot \
\
-t 2 \
cat <<-END_VERSIONS > versions.yml
"NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT":
nanoplot: $(echo $(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*$//')
END_VERSIONS
The call at the top, NanoPlot -t 2
, looks incomplete.
PS: For the logging, setting the environment variable NXF_DEBUG
gives me a similar output to yours:
$ NXF_DEBUG=3 nextflow run nf-core/nanoseq …
[…]
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (ONTDNAPIG001_R1)'
Caused by:
Process `NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT (ONTDNAPIG001_R1)` terminated with an error exit status (2)
Command executed:
NanoPlot \
\
-t 2 \
cat <<-END_VERSIONS > versions.yml
"NFCORE_NANOSEQ:NANOSEQ:QCFASTQ_NANOPLOT_FASTQC:NANOPLOT":
nanoplot: $(echo $(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*$//')
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
+++ for i in {1..7}
+++ '[' 18043364 -lt 17895908 ']'
+++ cpu_peak[i]=18043364
+++ for i in {1..7}
+++ '[' 145476 -lt 101036 ']'
+++ cpu_peak[i]=145476
+++ for i in {1..7}
+++ '[' 6446 -lt 4502 ']'
+++ cpu_peak[i]=6446
+++ for i in {1..7}
+++ '[' 274 -lt 272 ']'
+++ cpu_peak[i]=274
+++ '[' 3 = 1 ']'
+++ nxf_stat_ret=(${sum[*]})
+++ '[' 3 -lt 10 ']'
+++ timeout=1
+++ read -t 1 -r DONE
usage: NanoPlot [-h] [-v] [-t THREADS] [--verbose] [--store] [--raw] [--huge]
[-o OUTDIR] [--no_static] [-p PREFIX] [--tsv_stats]
[--info_in_report] [--maxlength N] [--minlength N]
[--drop_outliers] [--downsample N] [--loglength]
[--percentqual] [--alength] [--minqual N] [--runtime_until N]
[--readtype {1D,2D,1D2}] [--barcoded] [--no_supplementary]
[-c COLOR] [-cm COLORMAP]
[-f [{png,jpg,jpeg,webp,svg,pdf,eps,json} ...]]
[--plots [{kde,hex,dot} ...]] [--legacy [{kde,dot,hex} ...]]
[--listcolors] [--listcolormaps] [--no-N50] [--N50]
[--title TITLE] [--font_scale FONT_SCALE] [--dpi DPI]
executor > local (5)
The problem seem to be empty input_file
in the nanoplot module, when the last branch(?) is taken:
No idea how to easily debug this.
@gzentner, maybe you can update the issue title to module/nanoplot: Empty input_files
leads to incorrect NanoPlot call.
@paulmenzel - just a wild guess: our user's input_file
is named xxx001.fq.gz
.. nf-core/nanoplot/main.nf
looks for input file extensions ".fastq.gz" or ".txt" to deduce input type and thus to assign correct parameter, either --fastq
or --summary
.
If none of these extensions is found, input_file = ''
, is empty string.
That will cause NanoPlot
to fail ...
So we should either fix nf file or input file naming ...
Hi guys, I was also getting this error, when giving fq.gz file, instead of the expected fastq.gz file. I've slightly modified the nanoplot module file and created the relevant pull request for this. Changing the "def input_file" section to the below seem to have fixed it.
...
def input_file = ("$ontfile".endsWith(".fastq.gz") || "$ontfile".endsWith(".fq.gz")) ? "--fastq ${ontfile}" :
("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
...
Description of the bug
I am attempting to run Nanoseq on some direct RNA-seq data with the following command, and get the ensuing error regarding Nanoplot. The rest of the pipeline seems to work fine if Nanoplot is skipped, but I'd really like to have that read length information. Thanks!
Command used and terminal output
Relevant files
No response
System information
Nextflow version: 23.04.2 Hardware: AWS EC2 Executor: local Container engine: Docker Nanoseq version: 3.1.0