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_prokka.config
github-actions / JUnit Test Report
test_taxonomy_prokka
Assertion failed:
10 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:
Tsv false
Force restart with latest tmp false
Remove temporary files true
Compressed 1
Threads 2
Verbosity 3
08/12 17:17:25 [[1;32mNOTICE[0m] Downloading 1 item(s)
08/12 17:17:25 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/kalamari.tsv
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
b50637|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 248ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 462ms
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 17:18:01 [[1;32mNOTICE[0m] Downloading 1 item(s)
08/12 17:18:01 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
20963f|OK | 381MiB/s|tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Status Legend:
(OK):download completed.
Error: createbintaxonomy failed
Error: createtaxdb died
Command error:
647500K .......... .......... .......... .......... .......... 77.8M
647550K .......... .......... .......... .......... .......... 75.2M
647600K .......... .......... .......... .......... .......... 76.2M
647650K .......... .......... .......... .......... .......... 86.9M
647700K .......... .......... .......... .......... .......... 77.9M
647750K .......... .......... .......... .......... .......... 70.7M
647800K .......... .......... .......... .......... .......... 80.0M
647850K .......... .......... .......... .......... .......... 80.1M
647900K .......... .......... .......... .......... .......... 98.1M
647950K .......... .......... .......... .......... .......... 75.8M
648000K .......... .......... .......... .......... .......... 75.0M
648050K .......... .......... .......... .......... .......... 73.0M
648100K .......... .......... .......... .......... .......... 81.6M
648150K .......... .......... .......... .......... ... 73.4M=25s
2024-08-12 17:17:50 (25.3 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 248ms
Database type: Nucleotide
Time for processing: 0h 0m 4s 462ms
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 17:18:01 [[1;32mNOTICE[0m] Downloading 1 item(s)
08/12 17:18:01 [[1;32mNOTICE[0m] Download complete: tmp//10896966522998415356/taxonomy/taxdump.tar.gz
Download Results:
gid |stat|avg speed |path/URI
======+====+===========+=======================================================
20963f|OK | 381MiB/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.
Error: createbintaxonomy failed
tmp//10896966522998415356/taxonomy/createindex.sh: line 79: 1631 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/c695303b4920bdf3902ed74a6265a3c/work/28/86b5d0b5cbf835eaeb6f0018ec7225
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/funcscan/funcscan/.nf-test/tests/c695303b4920bdf3902ed74a6265a3c/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/c695303b4920bdf3902ed74a6265a3c/meta/nextflow.log' file for details
Nextflow stderr:
Loading