Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-c541f243d46d6f67954d724bf0afecd3.nf` [disturbed_kalam] DSL2 - revision: 9921031ec8
Downloading plugin [email protected]
Downloading plugin [email protected]
[05/f95b39] 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
  0cacab098358: Verifying Checksum
  0cacab098358: Download complete
  0cacab098358: Pull complete
  9ddd7f00c876: Verifying Checksum
  9ddd7f00c876: Download complete
  bd9ddc54bea9: Verifying Checksum
  bd9ddc54bea9: Download 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/c541f243d46d6f67954d724bf0afecd3/work/05/f95b39fbfef1101a44b1d479daf3b9

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

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/c541f243d46d6f67954d724bf0afecd3/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-c5049774cdd9c20838a28e4123d0172c.nf` [suspicious_golick] DSL2 - revision: 0c79a465a5
[46/193796] Submitted process > KALLISTO_INDEX (transcriptome.fasta)
ERROR ~ Error executing process > 'KALLISTO_INDEX (transcriptome.fasta)'

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


Command executed:

  kallisto \
      index \
      -k 31 \
      -i kallisto \
      transcriptome.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "KALLISTO_INDEX":
      kallisto: $(echo $(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0' locally
  0.51.1--heb0cbe2_0: Pulling from biocontainers/kallisto
  0cacab098358: Already exists
  bd9ddc54bea9: Already exists
  bd1705508a41: Pulling fs layer
  bd1705508a41: Verifying Checksum
  bd1705508a41: Download complete
  bd1705508a41: Pull complete
  Digest: sha256:b054a431d79c8f7ee65ee5fa0e9869da122b08bd669c957ed35dfca45ceacb39
  Status: Downloaded newer image for quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/c5049774cdd9c20838a28e4123d0172c/work/46/193796fc97b6baae06466611ba1b6c

Container:
  quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0

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/c5049774cdd9c20838a28e4123d0172c/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-f1645ec1dd2a083ebe4562bd203aa41.nf` [fabulous_payne] DSL2 - revision: 9921031ec8
[7f/37720f] 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/f1645ec1dd2a083ebe4562bd203aa41/work/7f/37720f7f061154a163308fb2284c7a

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/f1645ec1dd2a083ebe4562bd203aa41/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-3ae598839dba3c1f52d423f26306d59d.nf` [insane_carson] DSL2 - revision: 0c79a465a5
[dc/2f930d] Submitted process > KALLISTO_INDEX (transcriptome.fasta)
ERROR ~ Error executing process > 'KALLISTO_INDEX (transcriptome.fasta)'

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


Command executed:

  mkdir kallisto
  
  cat <<-END_VERSIONS > versions.yml
  "KALLISTO_INDEX":
      kallisto: $(echo $(kallisto 2>&1) | sed 's/^kallisto //; s/Usage.*$//')
  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/3ae598839dba3c1f52d423f26306d59d/work/dc/2f930d7325e9e0aa3732d26e885a17

Container:
  quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0

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/3ae598839dba3c1f52d423f26306d59d/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: