conda create issue

[acebollada80]

Description of feature

I am trying to test the pipeline and I have executed nextflow run nf-core/sarek -profile test,conda --outdir test_directory It starts running but returns the following error

Execution cancelled -- Finishing pending tasks before exit -[nf-core/sarek] Pipeline completed with errors- WARN: There's no process matching config selector: .:FREEC_SOMATIC -- Did you mean: FREEC_SOMATIC? WARN: There's no process matching config selector: .:FILTERVARIANTTRANCHES -- Did you mean: FILTERVARIANTTRANCHES? WARN: There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS? Error executing process > 'NFCORE_SAREK:SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome)'

Caused by: Process NFCORE_SAREK:SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED (genome) terminated with an error exit status (1)

Command executed:

gatk --java-options "-Xmx6g" IntervalListToBed --INPUT genome.interval_list --OUTPUT genome.bed --TMP_DIR . \

cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:PREPARE_INTERVALS:GATK4_INTERVALLISTTOBED": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.(GATK) v//; s/ .$//') END_VERSIONS

Command exit status: 1

Command output: (empty)

Command error: Error: Invalid or corrupt jarfile /home/bigan/miniconda3/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Using GATK jar /home/bigan/miniconda3/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6g -jar /home/bigan/miniconda3/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar IntervalListToBed --INPUT genome.interval_list --OUTPUT genome.bed --TMP_DIR .

Work dir: /home/bigan/work/32/d693bac63a16e84df3985d6f464104

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

The environment I am working in is a conda environment. I have checked the version of GATK and it is the latest 4.3.0 and the version of Java is also up to date. Can you please help me resolve this issue? Thank you.

[maxulysse]

Can you try removing this conda env and relaunching again. I've notice such errors in tests from time to time, and restarting usually works

[acebollada80]

I can't remove this conda environment because it is being used by other tools, but I can create a new conda environment to see if it runs correctly.

[maxulysse]

@acebollada80 any update on that issue?