Make genomic FASTA input optional #236
GitHub Actions / JUnit Test Report
failed
Jan 22, 2025 in 0s
2 tests run, 0 passed, 0 skipped, 2 failed.
Annotations
Check failure on line 1 in Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON
github-actions / JUnit Test Report
Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON.homo_sapiens paired-end [fastq]
java.lang.NullPointerException: Cannot invoke method getAt() on null object
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-1e7632216f13742126d0c16105de49f4.nf` [sharp_almeida] DSL2 - revision: 90a53586d8
Downloading plugin [email protected]
Downloading plugin [email protected]
[cb/dbfef4] Submitted process > SALMON_INDEX (transcriptome.fasta)
[c8/6c0724] Submitted process > FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (test)
ERROR ~ Error executing process > 'FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (test)'
Caused by:
Process `FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (test)` terminated with an error exit status (126)
Command executed:
fq subsample \
--record-count 1000000 --seed 1 \
test_1.fastq.gz test_2.fastq.gz \
--r1-dst test_R1.fastq.gz \
--r2-dst test_R2.fastq.gz
cat <<-END_VERSIONS > versions.yml
"FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE":
fq: $(echo $(fq subsample --version | sed 's/fq-subsample //g'))
END_VERSIONS
Command exit status:
126
Command output:
(empty)
Command error:
Unable to find image 'quay.io/biocontainers/fq:0.12.0--h9ee0642_0' locally
0.12.0--h9ee0642_0: Pulling from biocontainers/fq
0cacab098358: Already exists
bd9ddc54bea9: Already exists
71ed848086ad: Pulling fs layer
71ed848086ad: Verifying Checksum
71ed848086ad: Download complete
71ed848086ad: Pull complete
Digest: sha256:74b59572f1d05b4829b45b599ee04311c8b3acec510f3cfb879f23b4bbd2090b
Status: Downloaded newer image for quay.io/biocontainers/fq:0.12.0--h9ee0642_0
/bin/bash: line 10: .command.run: Permission denied
Work dir:
/home/runner/work/rnaseq/rnaseq/~/tests/1e7632216f13742126d0c16105de49f4/work/c8/6c0724b4577e68d7399879caaf3572
Container:
quay.io/biocontainers/fq:0.12.0--h9ee0642_0
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/1e7632216f13742126d0c16105de49f4/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
Check failure on line 1 in Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON
github-actions / JUnit Test Report
Test Workflow FASTQ_SUBSAMPLE_FQ_SALMON.homo_sapiens paired-end [fastq] - stub
java.lang.NullPointerException: Cannot invoke method getAt() on null object
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-fce4a6257b9f69dbf4794fffb7d2ee6e.nf` [disturbed_bhaskara] DSL2 - revision: 90a53586d8
[2e/317441] Submitted process > SALMON_INDEX (transcriptome.fasta)
[0e/d771e5] Submitted process > FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (test)
ERROR ~ Error executing process > 'SALMON_INDEX (transcriptome.fasta)'
Caused by:
Process `SALMON_INDEX (transcriptome.fasta)` terminated with an error exit status (126)
Command executed:
mkdir salmon
touch salmon/complete_ref_lens.bin
touch salmon/ctable.bin
touch salmon/ctg_offsets.bin
touch salmon/duplicate_clusters.tsv
touch salmon/info.json
touch salmon/mphf.bin
touch salmon/pos.bin
touch salmon/pre_indexing.log
touch salmon/rank.bin
touch salmon/refAccumLengths.bin
touch salmon/ref_indexing.log
touch salmon/reflengths.bin
touch salmon/refseq.bin
touch salmon/seq.bin
touch salmon/versionInfo.json
cat <<-END_VERSIONS > versions.yml
"SALMON_INDEX":
salmon: $(echo $(salmon --version) | sed -e "s/salmon //g")
END_VERSIONS
Command exit status:
126
Command output:
(empty)
Command error:
/bin/bash: line 10: .command.run: Permission denied
Work dir:
/home/runner/work/rnaseq/rnaseq/~/tests/fce4a6257b9f69dbf4794fffb7d2ee6e/work/2e/31744110f034d66f07894e2911d577
Container:
quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
-- Check '/home/runner/work/rnaseq/rnaseq/~/tests/fce4a6257b9f69dbf4794fffb7d2ee6e/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
Loading