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Make genomic FASTA input optional #236

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Make genomic FASTA input optional

Make genomic FASTA input optional #236

GitHub Actions / JUnit Test Report failed Jan 22, 2025 in 0s

8 tests run, 0 passed, 0 skipped, 8 failed.

Annotations

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - single_end 

Assertion failed: 

4 of 4 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-dddedf2a042d08ce57c225d3924c992b.nf` [romantic_kimura] DSL2 - revision: 9289b5727d
Downloading plugin [email protected]
Downloading plugin [email protected]
[fa/bc7845] 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
  bd9ddc54bea9: Verifying Checksum
  bd9ddc54bea9: Download complete
  0cacab098358: Verifying Checksum
  0cacab098358: Download complete
  0cacab098358: Pull complete
  bd9ddc54bea9: Pull complete
  9ddd7f00c876: Verifying Checksum
  9ddd7f00c876: Download 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/dddedf2a042d08ce57c225d3924c992b/work/fa/bc784544613b7598c8f9244312c89c

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/dddedf2a042d08ce57c225d3924c992b/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - single_end stub 

Assertion failed: 

4 of 4 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-c17f9ce91878bae64ba50298898f0b99.nf` [fabulous_miescher] DSL2 - revision: 9289b5727d
[6a/a3b425] 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/c17f9ce91878bae64ba50298898f0b99/work/6a/a3b425bcd2f55aac6620fbdb89b848

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/c17f9ce91878bae64ba50298898f0b99/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - single_end lib type A 

Assertion failed: 

4 of 4 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-2670e6736e196e572a4f47ab98143662.nf` [exotic_kimura] DSL2 - revision: 9f73b09048
[46/5c78bb] 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:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/2670e6736e196e572a4f47ab98143662/work/46/5c78bb862ba6b2288655a750894a57

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

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`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/2670e6736e196e572a4f47ab98143662/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - single_end lib type A stub 

Assertion failed: 

4 of 4 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-4fc99fd5de4d653a210577bfd1160fc2.nf` [romantic_ramanujan] DSL2 - revision: 9f73b09048
[c8/7c8606] 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/4fc99fd5de4d653a210577bfd1160fc2/work/c8/7c860692c88628ba717c9b892adb2f

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/4fc99fd5de4d653a210577bfd1160fc2/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - pair_end 

Assertion failed: 

4 of 4 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-8c2a769ba68f9d7435199d091f5825c3.nf` [hopeful_easley] DSL2 - revision: ec16cd9c07
[e3/00c2b9] 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:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/8c2a769ba68f9d7435199d091f5825c3/work/e3/00c2b9dd8c32f50de3fcf7c345de9a

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

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`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/8c2a769ba68f9d7435199d091f5825c3/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - pair_end stub 

Assertion failed: 

4 of 4 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-82ba1b16d9c58218e059a9340f9fe05b.nf` [serene_sax] DSL2 - revision: ec16cd9c07
[5f/e2a5f5] 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/82ba1b16d9c58218e059a9340f9fe05b/work/5f/e2a5f50f7e4488a2eb5b0f4f682fa7

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

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`

 -- Check '/home/runner/work/rnaseq/rnaseq/~/tests/82ba1b16d9c58218e059a9340f9fe05b/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - pair_end multiple 

Assertion failed: 

4 of 4 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-16b8f596bd843f3ee282b89cda506293.nf` [evil_bose] DSL2 - revision: 6a7a86b4d9
[55/0ae738] 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:
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/16b8f596bd843f3ee282b89cda506293/work/55/0ae738d7bedde42c7b3099c8f3099e

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/16b8f596bd843f3ee282b89cda506293/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

Check failure on line 1 in Test Process SALMON_QUANT

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test Process SALMON_QUANT.sarscov2 - pair_end multiple stub 

Assertion failed: 

4 of 4 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-4f80830b9553cd85cadba5300754b6aa.nf` [nice_mcclintock] DSL2 - revision: 6a7a86b4d9
[59/37bb1d] 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/4f80830b9553cd85cadba5300754b6aa/work/59/37bb1df04569484e228c74bf0e9e8d

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/4f80830b9553cd85cadba5300754b6aa/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:
View more details on GitHub Actions