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
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:
Loading