Fix hamronization fargene input #1337
GitHub Actions / JUnit Test Report
failed
Aug 12, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
Annotations
Check failure on line 1 in conf/test_taxonomy_bakta.config
github-actions / JUnit Test Report
test_taxonomy_bakta
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 2 \
--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 2
Verbosity 3
08/12 17:22:28 [[1;32mNOTICE[0m] Downloading 1 item(s)
08/12 17:22:28 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/kalamari.tsv
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
fef8a8|OK | 10MiB/s|tmp//10896966522998415356/kalamari.tsv
Status Legend:
(OK):download completed.
createdb tmp//10896966522998415356/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 235ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 243ms
prefixid mmseqs_database/database_h tmp//10896966522998415356/header_pref.tsv --tsv --threads 2 -v 3
[=================================================================] 225 0s 0ms
Time for merging to header_pref.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 1ms
Create directory tmp//10896966522998415356/taxonomy
createtaxdb mmseqs_database/database tmp//10896966522998415356/taxonomy --threads 2 -v 3
Download taxdump.tar.gz
08/12 17:23:12 [[1;32mNOTICE[0m] Downloading 1 item(s)
[#760217 5.5MiB/62MiB(8%) CN:2 DL:8.8MiB ETA:6s]
08/12 17:23:14 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
760217|OK | 41MiB/s|tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Status Legend:
(OK):download completed.
Error: createbintaxonomy failed
Error: createtaxdb died
Command error:
647550K .......... .......... .......... .......... .......... 42.0M
647600K .......... .......... .......... .......... .......... 86.2M
647650K .......... .......... .......... .......... .......... 78.8M
647700K .......... .......... .......... .......... .......... 78.9M
647750K .......... .......... .......... .......... .......... 33.6M
647800K .......... .......... .......... .......... .......... 2.03M
647850K .......... .......... .......... .......... .......... 34.1M
647900K .......... .......... .......... .......... .......... 82.3M
647950K .......... .......... .......... .......... .......... 79.5M
648000K .......... .......... .......... .......... .......... 12.7M
648050K .......... .......... .......... .......... .......... 72.6M
648100K .......... .......... .......... .......... .......... 80.6M
648150K .......... .......... .......... .......... ... 82.0M=33s
2024-08-12 17:23:02 (19.2 MB/s) - ‘tmp//10896966522998415356/kalamari.fasta.tmp’ saved [663750307]
createdb tmp//10896966522998415356/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 235ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 243ms
prefixid mmseqs_database/database_h tmp//10896966522998415356/header_pref.tsv --tsv --threads 2 -v 3
[=================================================================] 225 0s 0ms
Time for merging to header_pref.tsv: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 1ms
Create directory tmp//10896966522998415356/taxonomy
createtaxdb mmseqs_database/database tmp//10896966522998415356/taxonomy --threads 2 -v 3
Download taxdump.tar.gz
08/12 17:23:12 [[1;32mNOTICE[0m] Downloading 1 item(s)
[#760217 5.5MiB/62MiB(8%) CN:2 DL:8.8MiB ETA:6s]
08/12 17:23:14 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
760217|OK | 41MiB/s|tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Status Legend:
(OK):download completed.
mmseqs: malloc.c:2385: sysmalloc: Assertion `(old_top == initial_top (av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse (old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
tmp//10896966522998415356/taxonomy/createindex.sh: line 79: 1817 Aborted (core dumped) "${MMSEQS}" createbintaxonomy "${NCBITAXINFO}/names.dmp" "${NCBITAXINFO}/nodes.dmp" "${NCBITAXINFO}/merged.dmp" "${TAXDBNAME}_taxonomy" ${VERBOSITY_PAR}
Error: createbintaxonomy failed
Error: createtaxdb died
Work dir:
/home/runner/work/funcscan/funcscan/.nf-test/tests/f3c977ae4ed417ce557ca47f2e68d906/work/cc/e4698a004779dfc821ad0fa0b1aff4
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/f3c977ae4ed417ce557ca47f2e68d906/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/f3c977ae4ed417ce557ca47f2e68d906/meta/nextflow.log' file for details
Nextflow stderr:
Loading