Merge pull request #437 from nf-core/fix-rgi-db-name-issue #1439
GitHub Actions / JUnit Test Report
failed
Jan 16, 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_taxonomy_pyrodigal
Assertion failed:
16 of 17 assertions failed
Raw output
Nextflow stdout:
ERROR ~ Error executing process > 'NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_DATABASES (Kalamari)'
Caused by:
Process `NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_DATABASES (Kalamari)` terminated with an error exit status (1)
Command executed:
mkdir mmseqs_database/
mmseqs databases \
Kalamari \
mmseqs_database/database \
tmp/ \
--threads 4 \
--compressed 1 \
--remove-tmp-files
cat <<-END_VERSIONS > versions.yml
"NFCORE_FUNCSCAN:FUNCSCAN:TAXA_CLASS:MMSEQS_DATABASES":
mmseqs: $(mmseqs | grep 'Version' | sed 's/MMseqs2 Version: //')
END_VERSIONS
Command exit status:
1
Command output:
Force restart with latest tmp false
Remove temporary files true
Compressed 1
Threads 4
Verbosity 3
01/16 11:45:24 [[1;32mNOTICE[0m] Downloading 1 item(s)
01/16 11:45:24 [[1;32mNOTICE[0m] Download complete: tmp//12151822920407823486/kalamari.tsv
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
24f863|OK | 10MiB/s|tmp//12151822920407823486/kalamari.tsv
Status Legend:
(OK):download completed.
createdb tmp//12151822920407823486/kalamari.fasta mmseqs_database/database --compressed 1 -v 3
Converting sequences
[
Time for merging to database_h: 0h 0m 0s 2ms
Time for merging to database: 0h 0m 0s 176ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 27ms
prefixid mmseqs_database/database_h tmp//12151822920407823486/header_pref.tsv --tsv --threads 4 -v 3
[=================================================================] 225 0s 0ms
Time for merging to header_pref.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
Create directory tmp//12151822920407823486/taxonomy
createtaxdb mmseqs_database/database tmp//12151822920407823486/taxonomy --threads 4 -v 3
Download taxdump.tar.gz
01/16 11:46:06 [[1;32mNOTICE[0m] Downloading 1 item(s)
[#e9eb74 7.0MiB/64MiB(10%) CN:2 DL:12MiB ETA:4s]
01/16 11:46:08 [[1;32mNOTICE[0m] Download complete: tmp//12151822920407823486/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
e9eb74|OK | 48MiB/s|tmp//12151822920407823486/taxonomy/taxdump.tar.gz
Status Legend:
(OK):download completed.
Error: createbintaxonomy failed
Error: createtaxdb died
Command error:
647550K .......... .......... .......... .......... .......... 82.6M
647600K .......... .......... .......... .......... .......... 80.2M
647650K .......... .......... .......... .......... .......... 83.7M
647700K .......... .......... .......... .......... .......... 90.2M
647750K .......... .......... .......... .......... .......... 86.7M
647800K .......... .......... .......... .......... .......... 84.9M
647850K .......... .......... .......... .......... .......... 84.1M
647900K .......... .......... .......... .......... .......... 90.8M
647950K .......... .......... .......... .......... .......... 80.8M
648000K .......... .......... .......... .......... .......... 88.9M
648050K .......... .......... .......... .......... .......... 75.2M
648100K .......... .......... .......... .......... .......... 91.0M
648150K .......... .......... .......... .......... ... 85.0M=32s
2025-01-16 11:45:57 (19.7 MB/s) - ‘tmp//12151822920407823486/kalamari.fasta.tmp’ saved [663750307]
createdb tmp//12151822920407823486/kalamari.fasta mmseqs_database/database --compressed 1 -v 3
Converting sequences
[
Time for merging to database_h: 0h 0m 0s 2ms
Time for merging to database: 0h 0m 0s 176ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 27ms
prefixid mmseqs_database/database_h tmp//12151822920407823486/header_pref.tsv --tsv --threads 4 -v 3
[=================================================================] 225 0s 0ms
Time for merging to header_pref.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 2ms
Create directory tmp//12151822920407823486/taxonomy
createtaxdb mmseqs_database/database tmp//12151822920407823486/taxonomy --threads 4 -v 3
Download taxdump.tar.gz
01/16 11:46:06 [[1;32mNOTICE[0m] Downloading 1 item(s)
[#e9eb74 7.0MiB/64MiB(10%) CN:2 DL:12MiB ETA:4s]
01/16 11:46:08 [[1;32mNOTICE[0m] Download complete: tmp//12151822920407823486/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
e9eb74|OK | 48MiB/s|tmp//12151822920407823486/taxonomy/taxdump.tar.gz
Status Legend:
(OK):download completed.
double free or corruption (out)
Error: createbintaxonomy failed
tmp//12151822920407823486/taxonomy/createindex.sh: line 79: 1819 Aborted (core dumped) "${MMSEQS}" createbintaxonomy "${NCBITAXINFO}/names.dmp" "${NCBITAXINFO}/nodes.dmp" "${NCBITAXINFO}/merged.dmp" "${TAXDBNAME}_taxonomy" ${VERBOSITY_PAR}
Error: createtaxdb died
Work dir:
/home/runner/work/funcscan/funcscan/.nf-test/tests/237a9cc7d7305da4ae99f8a5873c779a/work/4b/a5e49e1c561f2590c9e47f68069fbd
Container:
quay.io/biocontainers/mmseqs2:15.6f452--pl5321h6a68c12_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/funcscan/funcscan/.nf-test/tests/237a9cc7d7305da4ae99f8a5873c779a/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/237a9cc7d7305da4ae99f8a5873c779a/meta/nextflow.log' file for details
Nextflow stderr:
Loading