Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/.nf-test-640affe0a1cb8973a6782fa01cd6d78.nf` [wise_booth] DSL2 - revision: 58cb1b06f6
Downloading plugin [email protected]
Downloading plugin [email protected]
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[ae/86cbb4] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/python:3.9--1' locally
  3.9--1: Pulling from biocontainers/python
  c1a16a04cedd: Pulling fs layer
  4ca545ee6d5d: Pulling fs layer
  5f7a6762e5ca: Pulling fs layer
  4ca545ee6d5d: Verifying Checksum
  4ca545ee6d5d: Download complete
  c1a16a04cedd: Verifying Checksum
  c1a16a04cedd: Download complete
  c1a16a04cedd: Pull complete
  4ca545ee6d5d: Pull complete
  5f7a6762e5ca: Verifying Checksum
  5f7a6762e5ca: Download complete
  5f7a6762e5ca: Pull complete
  Digest: sha256:d97d2b329b4e44d2e07a9737ba348b185d6a47f34fba0ef301d44d11669cac60
  Status: Downloaded newer image for quay.io/biocontainers/python:3.9--1
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/640affe0a1cb8973a6782fa01cd6d78/work/ae/86cbb493ce725cde2922ff19203858

Container:
  quay.io/biocontainers/python:3.9--1

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/640affe0a1cb8973a6782fa01cd6d78/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-fee9f28f43ac32ff0cfd1777afb06410.nf` [pedantic_descartes] DSL2 - revision: 58cb1b06f6
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[d2/383b38] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/fee9f28f43ac32ff0cfd1777afb06410/work/d2/383b38576b5047bf178cc03532dd0e

Container:
  quay.io/biocontainers/python:3.9--1

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/fee9f28f43ac32ff0cfd1777afb06410/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-ddb6453b557df370ed53d11b17893ba5.nf` [happy_gates] DSL2 - revision: 7fae19767d
[a0/d8e657] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
ERROR ~ Error executing process > 'PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)'

Caused by:
  Process `PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)` terminated with an error exit status (126)


Command executed [/home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/tests/../../../../modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py]:

  #!/usr/bin/env python3
  
  # Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license.
  
  import logging
  import os
  import platform
  from itertools import groupby
  from typing import Iterator, Tuple
  
  
  def setup_logging() -> logging.Logger:
      """Configure logging for the script.
  
      Returns:
          logging.Logger: Configured logger instance.
      """
      logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
      logger = logging.getLogger(__file__)
      logger.setLevel(logging.INFO)
      return logger
  
  
  def format_yaml_like(data: dict, indent: int = 0) -> str:
      """Formats a dictionary to a YAML-like string.
  
      Args:
          data (dict): The dictionary to format.
          indent (int): The current indentation level.
  
      Returns:
          str: A string formatted as YAML.
      """
      yaml_str = ""
      for key, value in data.items():
          spaces = "  " * indent
          if isinstance(value, dict):
              yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}"
          else:
              yaml_str += f"{spaces}{key}: {value}\n"
      return yaml_str
  
  
  def parse_fasta(fasta_file: str) -> Iterator[Tuple[str, str]]:
      """Parse a fasta file and yield tuples of header and sequence.
  
      Args:
          fasta_file (str): Path to the fasta file.
  
      Yields:
          Iterator[Tuple[str, str]]: Tuples of header and sequence from the fasta file.
  
  
      modified from Brent Pedersen
      Correct Way To Parse A Fasta File In Python
      given a fasta file. yield tuples of header, sequence
  
      Fasta iterator from https://www.biostars.org/p/710/#120760
      """
      with open(fasta_file) as file_handle:
          fasta_iter = (x[1] for x in groupby(file_handle, lambda line: line[0] == ">"))
          for header in fasta_iter:
              header_str = next(header)[1:].strip()
              sequence = "".join(s.strip() for s in next(fasta_iter))
              yield (header_str, sequence)
  
  
  def fasta_to_gtf(fasta: str, output_file: str, biotype: str) -> None:
      """
      Read a fasta file and create a GTF file.
  
      Args:
          fasta (str): Path to the fasta file.
          output_file (str): Path for the output GTF file.
          biotype (str): The biotype to use in the GTF.
      """
      fasta_iter = parse_fasta(fasta)
      lines = []
  
      for header, sequence in fasta_iter:
          seq_name = header.split()[0].replace(" ", "_")
          line = generate_gtf_line(seq_name, len(sequence), biotype)
          lines.append(line)
  
      with open(output_file, "w") as file_handle:
          file_handle.writelines(lines)
  
  
  def generate_gtf_line(name: str, length: int, biotype: str) -> str:
      """Generate a single GTF line given sequence name, length, and biotype.
  
      Args:
          name (str): Name of the sequence.
          length (int): Length of the sequence.
          biotype (str): Biotype of the sequence.
  
      Returns:
          str: A formatted GTF line.
      """
      biotype_attr = f' {biotype} "transgene";' if biotype else ""
      attributes = f'exon_id "{name}.1"; exon_number "1";{biotype_attr} gene_id "{name}_gene"; gene_name "{name}_gene"; gene_source "custom"; transcript_id "{name}_gene"; transcript_name "{name}_gene";\n'
      return f"{name}\ttransgene\texon\t1\t{length}\t.\t+\t.\t{attributes}"
  
  
  def main() -> None:
      # Parse arguments using argparse (not shown for brevity)
      # Example: args = parser.parse_args()
  
      logger = setup_logging()
      logger.info("Starting fasta to GTF conversion.")
  
      # Add fasta lines to GTF
      add_name = os.path.splitext(os.path.basename("gfp.fa"))[0]
      fasta_to_gtf("gfp.fa", f"{add_name}.gtf", "gene_biotype")
  
      # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF
      genome_name = "null" if "null" != "null" else os.path.splitext(os.path.basename("genome.fasta"))[0]
      output_prefix = "null" if "null" != "null" else f"{genome_name}_{add_name}"
  
      os.mkdir("out")
      os.system(f"cat genome.fasta gfp.fa > out/{output_prefix}.fasta")
      os.system(f"cat genes_with_empty_tid.gtf {add_name}.gtf > out/{output_prefix}.gtf")
  
      logger.info("Conversion completed successfully.")
  
      # Write the versions
      versions_this_module = {}
      versions_this_module["PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA"] = {"python": platform.python_version()}
      with open("versions.yml", "w") as f:
          f.write(format_yaml_like(versions_this_module))
  
  
  if __name__ == "__main__":
      main()

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/biocontainers/python:3.12' locally
  3.12: Pulling from biocontainers/python
  fa7e54f17dc0: Pulling fs layer
  4ca545ee6d5d: Pulling fs layer
  1c07fc5d4486: Pulling fs layer
  fa7e54f17dc0: Verifying Checksum
  fa7e54f17dc0: Download complete
  fa7e54f17dc0: Pull complete
  4ca545ee6d5d: Verifying Checksum
  4ca545ee6d5d: Download complete
  4ca545ee6d5d: Pull complete
  1c07fc5d4486: Verifying Checksum
  1c07fc5d4486: Download complete
  1c07fc5d4486: Pull complete
  Digest: sha256:29fccb317d61a9d09ecf432f63bfea512b98f0f3bc3764dc65fbdbc0f02473b5
  Status: Downloaded newer image for quay.io/biocontainers/python:3.12
  /bin/bash: line 10: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/ddb6453b557df370ed53d11b17893ba5/work/a0/d8e657fc19d715fbaf16941b7fc314

Container:
  quay.io/biocontainers/python:3.12

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/ddb6453b557df370ed53d11b17893ba5/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-45adf83fc482b2dcc3761b2644bad943.nf` [irreverent_neumann] DSL2 - revision: 7b440370f4
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[41/e11762] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/45adf83fc482b2dcc3761b2644bad943/work/41/e1176219dc225f11c10ad3d793e0e0

Container:
  quay.io/biocontainers/python:3.9--1

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/45adf83fc482b2dcc3761b2644bad943/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-6df1e190828956928df40c7201f2df4d.nf` [fabulous_lovelace] DSL2 - revision: 15679e67bc
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[ba/6116f2] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/6df1e190828956928df40c7201f2df4d/work/ba/6116f2df054283198b885f5d3ab348

Container:
  quay.io/biocontainers/python:3.9--1

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/6df1e190828956928df40c7201f2df4d/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-e55d6879442cae099ed51d5836af78f0.nf` [agitated_hoover] DSL2 - revision: f60bd538f1
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[fb/cfc7a8] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/e55d6879442cae099ed51d5836af78f0/work/fb/cfc7a8094765af8ee42e57fb593d86

Container:
  quay.io/biocontainers/python:3.9--1

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/e55d6879442cae099ed51d5836af78f0/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-99281af93c7b431e548a22c7c69cf8b0.nf` [intergalactic_cray] DSL2 - revision: 86ce425be1
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[31/e89743] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[f0/acec8f] Submitted process > PREPARE_GENOME:GFFREAD (null)
ERROR ~ Error executing process > 'PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)'

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


Command executed:

  cat transcriptome.fasta | cut -d "|" -f1 > transcriptome.fixed.fa
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE":
      sed: $(echo $(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  Unable to find image 'quay.io/nf-core/ubuntu:20.04' locally
  20.04: Pulling from nf-core/ubuntu
  99803d4b97f3: Pulling fs layer
  99803d4b97f3: Verifying Checksum
  99803d4b97f3: Download complete
  99803d4b97f3: Pull complete
  Digest: sha256:59e9d08d8dc153bfc704de15af5b14ac82f5ac695377fa29dd5087b6fea7942e
  Status: Downloaded newer image for quay.io/nf-core/ubuntu:20.04
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/99281af93c7b431e548a22c7c69cf8b0/work/31/e89743bba25e17dc6c04f713c86a9a

Container:
  quay.io/nf-core/ubuntu:20.04

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/99281af93c7b431e548a22c7c69cf8b0/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-fdd951cda87b113761f9bf37454ef2c.nf` [extravagant_escher] DSL2 - revision: e517c50d3b
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[92/03143b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/fdd951cda87b113761f9bf37454ef2c/work/92/03143be64e4ee9751d62a9171eccb3

Container:
  quay.io/biocontainers/python:3.9--1

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/fdd951cda87b113761f9bf37454ef2c/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-5e76b1622f3e89214ac015068690bb08.nf` [curious_hilbert] DSL2 - revision: 1d12e6b471
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[d4/b7101c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[8e/36ab1f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[b4/b611d2] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/5e76b1622f3e89214ac015068690bb08/work/8e/36ab1ff67fdc9cf6d40e188c0c6d48

Container:
  quay.io/biocontainers/python:3.9--1

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/5e76b1622f3e89214ac015068690bb08/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
[b4/b611d2] NOTE: Process `PREPARE_GENOME:BBMAP_BBSPLIT (null)` terminated with an error exit status (126) -- Execution is retried (1)
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-3d7dfab73fd069c29caa6b71b9200264.nf` [chaotic_wright] DSL2 - revision: 6cc6fb3913
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[16/6c9731] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/3d7dfab73fd069c29caa6b71b9200264/work/16/6c9731a2609e974f643bd77ce4027c

Container:
  quay.io/biocontainers/python:3.9--1

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/3d7dfab73fd069c29caa6b71b9200264/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-a5a7980d1f5930ed4379dfb7468df662.nf` [friendly_monod] DSL2 - revision: 91cf64590a
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[4b/533614] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/a5a7980d1f5930ed4379dfb7468df662/work/4b/5336143f22b966d099dfb7f1184125

Container:
  quay.io/biocontainers/python:3.9--1

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/a5a7980d1f5930ed4379dfb7468df662/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-270807ed7ba750f404689f9929cedd40.nf` [awesome_ekeblad] DSL2 - revision: a0be1cf02b
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[c3/248e95] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/270807ed7ba750f404689f9929cedd40/work/c3/248e9531e50140c47d395f22934437

Container:
  quay.io/biocontainers/python:3.9--1

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/270807ed7ba750f404689f9929cedd40/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-2c9dfa44f6c04cce1a94fb6c5574633f.nf` [zen_mercator] DSL2 - revision: 20531b3ae1
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[d5/bb7186] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/2c9dfa44f6c04cce1a94fb6c5574633f/work/d5/bb7186cd6d01982c08c4c22a9d2827

Container:
  quay.io/biocontainers/python:3.9--1

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/2c9dfa44f6c04cce1a94fb6c5574633f/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-acf450e4a243876e5f395973f8895a51.nf` [scruffy_thompson] DSL2 - revision: 2d29c06d62
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[5f/93865d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/acf450e4a243876e5f395973f8895a51/work/5f/93865d36b4163165df4964eeae6b9f

Container:
  quay.io/biocontainers/python:3.9--1

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/acf450e4a243876e5f395973f8895a51/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-5a326afcb0cdf6699a393b9faa27f56d.nf` [extravagant_carlsson] DSL2 - revision: 9fcbb707d7
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[48/b7c770] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4b/03c7f8] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/5a326afcb0cdf6699a393b9faa27f56d/work/48/b7c770451fdd8b335c06d432f3901e

Container:
  quay.io/biocontainers/python:3.9--1

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/5a326afcb0cdf6699a393b9faa27f56d/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-223d2c56c3bdbd48b1200e3e6d5486b4.nf` [reverent_engelbart] DSL2 - revision: 4ec53411b2
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[94/41aa4c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/223d2c56c3bdbd48b1200e3e6d5486b4/work/94/41aa4c1bf8b5a2cec85f634a4d8d3c

Container:
  quay.io/biocontainers/python:3.9--1

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/223d2c56c3bdbd48b1200e3e6d5486b4/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-35d5b512ff1d0997b0fb586e3e322521.nf` [grave_leavitt] DSL2 - revision: 7fae19767d
[41/3b4137] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
ERROR ~ Error executing process > 'PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)'

Caused by:
  Process `PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)` terminated with an error exit status (126)


Command executed [/home/runner/work/rnaseq/rnaseq/subworkflows/local/prepare_genome/tests/../../../../modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py]:

  #!/usr/bin/env python3
  
  # Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license.
  
  import logging
  import os
  import platform
  from itertools import groupby
  from typing import Iterator, Tuple
  
  
  def setup_logging() -> logging.Logger:
      """Configure logging for the script.
  
      Returns:
          logging.Logger: Configured logger instance.
      """
      logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
      logger = logging.getLogger(__file__)
      logger.setLevel(logging.INFO)
      return logger
  
  
  def format_yaml_like(data: dict, indent: int = 0) -> str:
      """Formats a dictionary to a YAML-like string.
  
      Args:
          data (dict): The dictionary to format.
          indent (int): The current indentation level.
  
      Returns:
          str: A string formatted as YAML.
      """
      yaml_str = ""
      for key, value in data.items():
          spaces = "  " * indent
          if isinstance(value, dict):
              yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}"
          else:
              yaml_str += f"{spaces}{key}: {value}\n"
      return yaml_str
  
  
  def parse_fasta(fasta_file: str) -> Iterator[Tuple[str, str]]:
      """Parse a fasta file and yield tuples of header and sequence.
  
      Args:
          fasta_file (str): Path to the fasta file.
  
      Yields:
          Iterator[Tuple[str, str]]: Tuples of header and sequence from the fasta file.
  
  
      modified from Brent Pedersen
      Correct Way To Parse A Fasta File In Python
      given a fasta file. yield tuples of header, sequence
  
      Fasta iterator from https://www.biostars.org/p/710/#120760
      """
      with open(fasta_file) as file_handle:
          fasta_iter = (x[1] for x in groupby(file_handle, lambda line: line[0] == ">"))
          for header in fasta_iter:
              header_str = next(header)[1:].strip()
              sequence = "".join(s.strip() for s in next(fasta_iter))
              yield (header_str, sequence)
  
  
  def fasta_to_gtf(fasta: str, output_file: str, biotype: str) -> None:
      """
      Read a fasta file and create a GTF file.
  
      Args:
          fasta (str): Path to the fasta file.
          output_file (str): Path for the output GTF file.
          biotype (str): The biotype to use in the GTF.
      """
      fasta_iter = parse_fasta(fasta)
      lines = []
  
      for header, sequence in fasta_iter:
          seq_name = header.split()[0].replace(" ", "_")
          line = generate_gtf_line(seq_name, len(sequence), biotype)
          lines.append(line)
  
      with open(output_file, "w") as file_handle:
          file_handle.writelines(lines)
  
  
  def generate_gtf_line(name: str, length: int, biotype: str) -> str:
      """Generate a single GTF line given sequence name, length, and biotype.
  
      Args:
          name (str): Name of the sequence.
          length (int): Length of the sequence.
          biotype (str): Biotype of the sequence.
  
      Returns:
          str: A formatted GTF line.
      """
      biotype_attr = f' {biotype} "transgene";' if biotype else ""
      attributes = f'exon_id "{name}.1"; exon_number "1";{biotype_attr} gene_id "{name}_gene"; gene_name "{name}_gene"; gene_source "custom"; transcript_id "{name}_gene"; transcript_name "{name}_gene";\n'
      return f"{name}\ttransgene\texon\t1\t{length}\t.\t+\t.\t{attributes}"
  
  
  def main() -> None:
      # Parse arguments using argparse (not shown for brevity)
      # Example: args = parser.parse_args()
  
      logger = setup_logging()
      logger.info("Starting fasta to GTF conversion.")
  
      # Add fasta lines to GTF
      add_name = os.path.splitext(os.path.basename("gfp.fa"))[0]
      fasta_to_gtf("gfp.fa", f"{add_name}.gtf", "gene_biotype")
  
      # Concatenate new fasta to existing fasta, and the GTF we just generated to the GTF
      genome_name = "null" if "null" != "null" else os.path.splitext(os.path.basename("genome.fasta"))[0]
      output_prefix = "null" if "null" != "null" else f"{genome_name}_{add_name}"
  
      os.mkdir("out")
      os.system(f"cat genome.fasta gfp.fa > out/{output_prefix}.fasta")
      os.system(f"cat genes_with_empty_tid.gtf {add_name}.gtf > out/{output_prefix}.gtf")
  
      logger.info("Conversion completed successfully.")
  
      # Write the versions
      versions_this_module = {}
      versions_this_module["PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA"] = {"python": platform.python_version()}
      with open("versions.yml", "w") as f:
          f.write(format_yaml_like(versions_this_module))
  
  
  if __name__ == "__main__":
      main()

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/35d5b512ff1d0997b0fb586e3e322521/work/41/3b4137c43e446451571214423a231d

Container:
  quay.io/biocontainers/python:3.12

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/35d5b512ff1d0997b0fb586e3e322521/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-fcd803d34450eec01f89b24ab4aab8ec.nf` [chaotic_linnaeus] DSL2 - revision: 7b440370f4
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[50/b1375c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/fcd803d34450eec01f89b24ab4aab8ec/work/50/b1375cf199eb754f8cb64fefa644f2

Container:
  quay.io/biocontainers/python:3.9--1

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/fcd803d34450eec01f89b24ab4aab8ec/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-66bebf46f804014f4d94fadda85e3aea.nf` [golden_panini] DSL2 - revision: 15679e67bc
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[14/e02e80] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/66bebf46f804014f4d94fadda85e3aea/work/14/e02e80bbdfc0742bf85c476c7ee18e

Container:
  quay.io/biocontainers/python:3.9--1

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/66bebf46f804014f4d94fadda85e3aea/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-fb5ab8fb88b00de6e7db87f06483c819.nf` [modest_lichterman] DSL2 - revision: f60bd538f1
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[cd/f7d75d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  filter_gtf.py \
      --gtf genes_with_empty_tid.gtf \
      --fasta genome.fasta \
      --prefix genes_with_empty_tid
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/fb5ab8fb88b00de6e7db87f06483c819/work/cd/f7d75d10b8311985c7b6707903c967

Container:
  quay.io/biocontainers/python:3.9--1

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/fb5ab8fb88b00de6e7db87f06483c819/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-cb19c340befee22695d1e0884023e9c7.nf` [cheesy_cori] DSL2 - revision: 58cb1b06f6
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[2c/52bb9b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  touch genome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/cb19c340befee22695d1e0884023e9c7/work/2c/52bb9bd88c01e39d26ae60c9783bc8

Container:
  quay.io/biocontainers/python:3.9--1

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/cb19c340befee22695d1e0884023e9c7/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-7e31db8951465e0982e92789ec953d54.nf` [naughty_jennings] DSL2 - revision: 58cb1b06f6
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[19/9a98f7] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  touch genome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/7e31db8951465e0982e92789ec953d54/work/19/9a98f7e7d1c253418e702eaa88894b

Container:
  quay.io/biocontainers/python:3.9--1

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/7e31db8951465e0982e92789ec953d54/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-56b225c2ec3f38cee755aac78e120b69.nf` [chaotic_leavitt] DSL2 - revision: 7fae19767d
[d9/28eb28] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
ERROR ~ Error executing process > 'PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)'

Caused by:
  Process `PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)` terminated with an error exit status (126)


Command executed:

  mkdir out
  touch out/genome_transcriptome.fasta
  touch out/genome_transcriptome.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA":
      python: $(python --version | grep -v "Python ")
  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/56b225c2ec3f38cee755aac78e120b69/work/d9/28eb28d492979bfb534e91318494de

Container:
  quay.io/biocontainers/python:3.12

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/56b225c2ec3f38cee755aac78e120b69/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-83dd331574790256e72e5c103bc5379d.nf` [cheeky_leakey] DSL2 - revision: 7b440370f4
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[ca/222a8d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  touch genome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/83dd331574790256e72e5c103bc5379d/work/ca/222a8d1141ac65670e6abd1cc67ee1

Container:
  quay.io/biocontainers/python:3.9--1

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/83dd331574790256e72e5c103bc5379d/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-1a8315886038f3425e1f2afdb7212f32.nf` [distraught_morse] DSL2 - revision: 15679e67bc
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[a1/625bc8] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
ERROR ~ Error executing process > 'PREPARE_GENOME:GTF_FILTER (genome.fasta)'

Caused by:
  Process `PREPARE_GENOME:GTF_FILTER (genome.fasta)` terminated with an error exit status (126)


Command executed:

  touch genome.filtered.gtf
  
  cat <<-END_VERSIONS > versions.yml
  "PREPARE_GENOME:GTF_FILTER":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  /bin/bash: line 9: .command.run: Permission denied

Work dir:
  /home/runner/work/rnaseq/rnaseq/~/tests/1a8315886038f3425e1f2afdb7212f32/work/a1/625bc80db0054ac6258ebebe48b20b

Container:
  quay.io/biocontainers/python:3.9--1

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/1a8315886038f3425e1f2afdb7212f32/meta/nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit
Nextflow stderr: