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Ensure checking dbs filepaths exist #87

Ensure checking dbs filepaths exist

Ensure checking dbs filepaths exist #87

GitHub Actions / JUnit Test Report failed Jan 28, 2025 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Test pipeline: NFCORE_FUNCSCAN

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline: NFCORE_FUNCSCAN.test_nothing_profile

Assertion failed: 

2 of 3 assertions failed
Raw output
Nextflow stdout:

########## FINISHED GUINZIPPING ################# 
########## DID NOT FILTER ################# 
########## DID NOT ANNOTATE ################# 
########## DID NOT TAX CLASS ################# 
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP (sample_1.fasta.gz)'

Caused by:
  Process `NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP (sample_1.fasta.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      sample_1.fasta.gz \
      > sample_1.fasta
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FUNCSCAN:FUNCSCAN:GUNZIP_INPUT_PREP":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  2fc3b27fe229: Pulling fs layer
  4f4fb700ef54: Waiting
  2fc3b27fe229: Waiting
  92dc97a3ef36: Waiting
  10b8c00c10a5: Waiting
  bb36d6c3110d: Waiting
  0ea1a16bbe82: Waiting
  030a47592a0a: Waiting
  9f0d519e5362: Waiting
  17dc7ea432cc: Waiting
  dec6b097362e: Verifying Checksum
  dec6b097362e: Download complete
  f88da01cff0b: Verifying Checksum
  f88da01cff0b: Download complete
  dafa2b0c44d2: Verifying Checksum
  dafa2b0c44d2: Download complete
  4f4fb700ef54: Verifying Checksum
  4f4fb700ef54: Download complete
  92dc97a3ef36: Verifying Checksum
  92dc97a3ef36: Download complete
  403f74b0f85e: Download complete
  17dc7ea432cc: Verifying Checksum
  17dc7ea432cc: Download complete
  10b8c00c10a5: Verifying Checksum
  10b8c00c10a5: Download complete
  bb36d6c3110d: Download complete
  dafa2b0c44d2: Pull complete
  dec6b097362e: Pull complete
  0ea1a16bbe82: Verifying Checksum
  0ea1a16bbe82: Download complete
  030a47592a0a: Verifying Checksum
  030a47592a0a: Download complete
  f88da01cff0b: Pull complete
  4f4fb700ef54: Pull complete
  92dc97a3ef36: Pull complete
  403f74b0f85e: Pull complete
  10b8c00c10a5: Pull complete
  17dc7ea432cc: Pull complete
  bb36d6c3110d: Pull complete
  0ea1a16bbe82: Pull complete
  030a47592a0a: Pull complete
  9f0d519e5362: Verifying Checksum
  9f0d519e5362: Download complete
  9f0d519e5362: Pull complete
  2fc3b27fe229: Verifying Checksum
  2fc3b27fe229: Download complete
  2fc3b27fe229: Pull complete
  Digest: sha256:63c2c6b22e83b2f656e88fbb1553e595da4e9e58794e3bfcb98b20b3837f328a
  Status: Downloaded newer image for community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8
  /bin/bash: line 11: .command.run: Permission denied

Work dir:
  /home/runner/work/funcscan/funcscan/.nf-test/tests/4a4ce8e7eb32baadbf3dde2e85b8c915/work/17/0cecdd5bf95f5d7f0cbe811bf25063

Container:
  community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8

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/funcscan/funcscan/.nf-test/tests/4a4ce8e7eb32baadbf3dde2e85b8c915/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/funcscan/funcscan/.nf-test/tests/4a4ce8e7eb32baadbf3dde2e85b8c915/meta/nextflow.log' file for details
Nextflow stderr: