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Make genomic FASTA input optional #235

Make genomic FASTA input optional

Make genomic FASTA input optional #235

GitHub Actions / JUnit Test Report failed Jan 21, 2025 in 0s

3 tests run, 0 passed, 0 skipped, 3 failed.

Annotations

Check failure on line 1 in Test Process SALMON_INDEX

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_INDEX.sarscov2

Assertion failed: 

3 of 3 assertions failed
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-71306d1e06136cc0e441565a2c4c638a.nf` [soggy_fourier] DSL2 - revision: 240fbd414e
Downloading plugin [email protected]
Downloading plugin [email protected]
[7d/ffc78f] Submitted process > SALMON_INDEX (transcriptome.fasta)
ERROR ~ Error executing process > 'SALMON_INDEX (transcriptome.fasta)'

Caused by:
  Process `SALMON_INDEX (transcriptome.fasta)` terminated with an error exit status (126)


Command executed:

  if [ -n 'genome.fasta' ]; then
      grep '^>' genome.fasta | cut -d ' ' -f 1 | cut -d $'\t' -f 1 | sed 's/>//g' > decoys.txt
      cat transcriptome.fasta genome.fasta > gentrome.fa
  fi
  
  salmon \
      index \
      --threads 2 \
      -t gentrome.fa \
      -d decoys.txt \
      -k 31 \
      -i salmon
  
  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:
  Unable to find image 'quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2' locally
  1.10.3--h6dccd9a_2: Pulling from biocontainers/salmon
  0cacab098358: Pulling fs layer
  bd9ddc54bea9: Pulling fs layer
  9ddd7f00c876: Pulling fs layer
  9ddd7f00c876: Verifying Checksum
  9ddd7f00c876: Download complete
  bd9ddc54bea9: Verifying Checksum
  bd9ddc54bea9: Download complete
  0cacab098358: Verifying Checksum
  0cacab098358: Download complete
  0cacab098358: Pull complete
  bd9ddc54bea9: Pull complete
  9ddd7f00c876: Pull complete
  Digest: sha256:f83ebb158845ee8138d793347f83b92c75e83c58dd8f4600c6fea2a2453ef08e
  Status: Downloaded newer image for quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/71306d1e06136cc0e441565a2c4c638a/work/7d/ffc78fbadae7eb11985347d5da1009

Container:
  quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/71306d1e06136cc0e441565a2c4c638a/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_INDEX

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_INDEX.sarscov2 transcriptome only

Assertion failed: 

3 of 3 assertions failed
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-295ccf3bcb93b6c8ecae2fb98b26d149.nf` [dreamy_rutherford] DSL2 - revision: 6227954741
[88/db9601] Submitted process > SALMON_INDEX (transcriptome.fasta)
ERROR ~ Error executing process > 'SALMON_INDEX (transcriptome.fasta)'

Caused by:
  Process `SALMON_INDEX (transcriptome.fasta)` terminated with an error exit status (126)


Command executed:

  if [ -n '' ]; then
      grep '^>'  | cut -d ' ' -f 1 | cut -d $'\t' -f 1 | sed 's/>//g' > decoys.txt
      cat transcriptome.fasta  > transcriptome.fasta
  fi
  
  salmon \
      index \
      --threads 2 \
      -t transcriptome.fasta \
       \
      -k 31 \
      -i salmon
  
  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/295ccf3bcb93b6c8ecae2fb98b26d149/work/88/db9601e8f63c93464c70759ca98fab

Container:
  quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/295ccf3bcb93b6c8ecae2fb98b26d149/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_INDEX

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_INDEX.sarscov2 stub

Assertion failed: 

3 of 3 assertions failed
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-7fd95bbf35cf50c11814716911fd378a.nf` [mighty_woese] DSL2 - revision: 240fbd414e
[23/c141af] Submitted process > SALMON_INDEX (transcriptome.fasta)
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/7fd95bbf35cf50c11814716911fd378a/work/23/c141af8b2d2f2cf634ea7965cde059

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/7fd95bbf35cf50c11814716911fd378a/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: