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Conda profile FastQC crash #67
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Could be related to bioconda/bioconda-recipes#5026 |
Looks to me a bit like a bioconda issue |
Apparently its an issue if you have reversed conda channels.
is the correct order. I had the latter two switched, thus potentially causing that issue. I'll run a local test with the updated recipe and might push a new release to resolve the problem if that helps! |
Could you give it a try please @jfy133 ? Please use the switch |
Sadly same error. Also with fresh nextflow depencies and nf-core/eager2 files |
I have a similar issue on a Slurm based cluster, and reproduced the issue using conda, and singularity with a pre-build image (singularity pull) as well as a build image on the system itself. Here's the command and the error message:
|
The @jfy133 Can you test again in ~1 hour maybe using the @yassineS I opened a new issue for you #68 and will continue there. Its something else than this error actually.. |
This is fixed in release 2.0.1 #69 |
Describe the bug
When using the following flag
-profile standard,conda
the pipeline crashes atFastQC
with th exit status 127, and the following command error:Furthermore, one 'Tip' message provided is to check
.command.out
file in the work directory. However, this file doesn't exist. Note, the tip message seems to change when re-running so it would be good to know if this is a random 'help of the day' type message from Nextflow, and if so make that clearer.To Reproduce
The command I used was
run nf-core/eager --reads 'EXB015.A1701/*_R{1,2}*fastq.gz' --pairedEnd --fasta '~References/hg19_MT.fasta' -profile standard,conda --max_cpus 4 --max_memory 32G
(Sending input files privately)
Expected behavior
Not to crash and possibly for the conda environment downloaded having the correct library contents
Screenshots
NA
Operating System:
Ubuntu 14.04
Additional context
Please provide me with the following files:
.nextflow.log
results/pipeline_info/...
eager2_error_20181018.tar.gz
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