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` [happy_kare] DSL2 - revision: 240fbd414e
Downloading plugin [email protected]
Downloading plugin [email protected]
[92/503690] 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/71306d1e06136cc0e441565a2c4c638a/work/92/503690e0e5562fd425d744664eb6a4

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/71306d1e06136cc0e441565a2c4c638a/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

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` [intergalactic_dijkstra] DSL2 - revision: 6227954741
[37/a56eda] 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/37/a56eda8bf214d74611652362a7f28e

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/295ccf3bcb93b6c8ecae2fb98b26d149/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr:

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` [desperate_jang] DSL2 - revision: 240fbd414e
[4c/743efd] 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/4c/743efd1502d9caedb5e2239242ddac

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