SILVA database error: Process prepare_databases:prepareSILVA terminated with an error exit status (1) #148
Description
Operating System
Windows 11
Other Linux
Ubuntu 24.04.2 LTS (GNU/Linux 6.8.0-57-generic x86_64)
Workflow Version
v2.14.1
Workflow Execution
Command line (Local)
Other workflow execution
Within MobaXterm OpenStack Virtual Machine
EPI2ME Version
No response
CLI command run
sudo ./nextflow run epi2me-labs/wf-metagenomics --fastq 'wf-metagenomics-demo/test_data' -profile standard --database_set SILVA_138_1 --min_len 1200 --threads 8 --include_read_assignments True --output_unclassified True --amr True
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
Error in preparing Silva database despite update to the latest versions of Nextflow and wf/metagenomics.
Relevant log output
N E X T F L O W ~ version 25.10.2
Launching `https://github.com/epi2me-labs/wf-metagenomics` [lonely_celsius] DSL2 - revision: 8c6ba7d184 [master]
|||||||||| _____ ____ ___ ____ __ __ _____
|||||||||| | ____| _ \_ _|___ \| \/ | ____|
||||| | _| | |_) | | __) | |\/| | _|
||||| | |___| __/| | / __/| | | | |__
|||||||||| |_____|_| |___|_____|_| |_|_____|
|||||||||| wf-metagenomics v2.14.1-g8c6ba7d
--------------------------------------------------------------------------------
Core Nextflow options
revision : master
runName : lonely_celsius
containerEngine : docker
container : [withLabel:wfmetagenomics:ontresearch/wf-metagenomics:sha1d71a4d15f57a1c32aacdb94cacdeb268205548e, withLabel:wf_common:ontresearch/wf-common:sha72f3517dd994984e0e2da0b97cb3f23f8540be4b, withLabel:amr:ontresearch/abricate:shad8ebf2fc3b15d43612df71170bdd4d8669fe1731]
launchDir : /home/sarah
workDir : /home/sarah/work
projectDir : /root/.nextflow/assets/epi2me-labs/wf-metagenomics
userName : root
profile : standard
configFiles : /root/.nextflow/assets/epi2me-labs/wf-metagenomics/nextflow.config
Input Options
fastq : wf-metagenomics-demo/test_data
Reference Options
database_set : SILVA_138_1
Antimicrobial Resistance Options
amr : true
Output Options
include_read_assignments: true
output_unclassified : true
Advanced Options
min_len : 1200
threads : 8
!! Only displaying parameters that differ from the pipeline defaults !!
--------------------------------------------------------------------------------
If you use epi2me-labs/wf-metagenomics for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
--------------------------------------------------------------------------------
This is epi2me-labs/wf-metagenomics v2.14.1-g8c6ba7d.
--------------------------------------------------------------------------------
Checking inputs.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
[- ] fastcat -
[- ] fastcat -
executor > local (1)
executor > local (5)
executor > local (5)
executor > local (5)
executor > local (6)
executor > local (6)
executor > local (11)
[1b/d75c2d] fastcat (2) | 3 of 3 ✔
[10/756471] getVersions | 1 of 1 ✔
[1d/6691a8] getVersionsCommon | 1 of 1 ✔
[ca/efd962] getParams | 1 of 1 ✔
[bc/3bdc9a] prepare_databases:prepareSILVA | 0 of 1
[- ] prepare_databases:determine_bracken_length -
[- ] kraken_pipeline:run_kraken2 -
[- ] kraken_pipeline:run_bracken -
[- ] kraken_pipeline:createAbundanceTables -
[- ] kraken_pipeline:output_kraken2_read_assignments -
[26/039378] run_amr:abricate (barcode01) | 0 of 3
[- ] run_amr:abricate_json -
[5f/3c6d50] abricateVersion | 1 of 1 ✔
[- ] makeReport -
ERROR ~ Error executing process > 'prepare_databases:prepareSILVA'
Caused by:
Process `prepare_databases:prepareSILVA` terminated with an error exit status (1)
Command executed:
kraken2-build --db SILVA_138_1 --special silva
bracken-build -d SILVA_138_1 -t "2" -l 1000
# Move all the files following other default databases:
mkdir database
mv SILVA_138_1/*.k2d database/
mv SILVA_138_1/library/silva.fna database/
mv SILVA_138_1/seqid2taxid.map .
mv SILVA_138_1/taxonomy taxonomy
mv SILVA_138_1/database1000mers.kmer_distrib database/
Command exit status:
1
Command output:
491000 sequences read
492000 sequences read
493000 sequences read
494000 sequences read
495000 sequences read
496000 sequences read
497000 sequences read
498000 sequences read
499000 sequences read
500000 sequences read
501000 sequences read
502000 sequences read
503000 sequences read
504000 sequences read
505000 sequences read
506000 sequences read
507000 sequences read
508000 sequences read
509000 sequences read
510000 sequences read
510508 total sequences read
>>STEP 2: READING NODES.DMP FILE
0 nodes read
1000 nodes read
2000 nodes read
3000 nodes read
4000 nodes read
5000 nodes read
6000 nodes read
7000 nodes read
8000 nodes read
9000 nodes read
10000 nodes read
11000 nodes read
12000 nodes read
12923 total nodes read
>>STEP 3: CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS:
1000mers, with a database built using 35mers
Time Elaped: 1 minutes, 41 seconds, 0.00000 microseconds
=============================
PROGRAM START TIME: 01-12-2026 11:55:21
...11173 total genomes read from kraken output file
...creating kmer counts file -- lists the number of kmers of each classification per genome
...creating kmer distribution file -- lists genomes and kmer counts contributing to each genome
PROGRAM END TIME: 01-12-2026 11:55:21
Finished creating database1000mers.kraken and database1000mers.kmer_distrib [in DB folder]
*NOTE: to create read distribution files for multiple read lengths,
rerun this script specifying the same database but a different read length
Bracken build complete.
Command error:
510474 sequences converted (finished: LAYC01000003.3856081.3857875)
510475 sequences converted (finished: LKCM01000080.3673.5139)
510476 sequences converted (finished: LASS02003325.4070.5829)
510477 sequences converted (finished: LKUO01000978.8556.10127)
510478 sequences converted (finished: LKUO01003660.7536.9273)
510479 sequences converted (finished: LKUO01003983.25739.27486)
510480 sequences converted (finished: LKUO01004252.6799.8575)
510481 sequences converted (finished: LKUO01004410.7759.9532)
510482 sequences converted (finished: LKUO01004768.11583.13337)
510483 sequences converted (finished: LKUO01004890.22932.24655)
510484 sequences converted (finished: LKUO01005274.897.2663)
510485 sequences converted (finished: LKUO01005140.3744.5530)
510486 sequences converted (finished: LKUO01005616.1.1515)
510487 sequences converted (finished: LKMJ01012234.3184.4646)
510488 sequences converted (finished: LKUO01005795.13826.15972)
510489 sequences converted (finished: LKLZ01000003.1585553.1586832)
510490 sequences converted (finished: LKHX01005117.37952.39807)
510491 sequences converted (finished: LKHY01004835.24824.26669)
510492 sequences converted (finished: LUUB01000105.358.1856)
510493 sequences converted (finished: LUVW01000002.45778.47642)
510494 sequences converted (finished: JOCQ01000207.3420.4908)
510495 sequences converted (finished: JOIY01000094.204.1673)
510496 sequences converted (finished: JOMH01000001.1092401.1093910)
510497 sequences converted (finished: MHEE01000002.15960.17497)
510498 sequences converted (finished: MHYR01000121.4583.6167)
510499 sequences converted (finished: CFFF01000203.442.2194)
510500 sequences converted (finished: JENB01000091.335.1842)
510501 sequences converted (finished: CXYW01000009.360.1734)
510502 sequences converted (finished: CXWL01024289.1436.2731)
510503 sequences converted (finished: CXWK01001735.4041.5385)
510504 sequences converted (finished: MVBC01000034.3.1520)
executor > local (11)
[1b/d75c2d] fastcat (2) | 3 of 3 ✔
[10/756471] getVersions | 1 of 1 ✔
[1d/6691a8] getVersionsCommon | 1 of 1 ✔
[ca/efd962] getParams | 1 of 1 ✔
[bc/3bdc9a] prepare_databases:prepareSILVA | 0 of 1
[- ] prepare_databases:determine_bracken_length -
[- ] kraken_pipeline:run_kraken2 -
[- ] kraken_pipeline:run_bracken -
[- ] kraken_pipeline:createAbundanceTables -
[- ] kraken_pipeline:output_kraken2_read_assignments -
[26/039378] run_amr:abricate (barcode01) | 0 of 3
[- ] run_amr:abricate_json -
[5f/3c6d50] abricateVersion | 1 of 1 ✔
[- ] makeReport -
WARN: Killing running tasks (3)
ERROR ~ Error executing process > 'prepare_databases:prepareSILVA'
Caused by:
Process `prepare_databases:prepareSILVA` terminated with an error exit status (1)
Command executed:
kraken2-build --db SILVA_138_1 --special silva
bracken-build -d SILVA_138_1 -t "2" -l 1000
# Move all the files following other default databases:
mkdir database
mv SILVA_138_1/*.k2d database/
mv SILVA_138_1/library/silva.fna database/
mv SILVA_138_1/seqid2taxid.map .
mv SILVA_138_1/taxonomy taxonomy
mv SILVA_138_1/database1000mers.kmer_distrib database/
Command exit status:
1
Command output:
491000 sequences read
492000 sequences read
493000 sequences read
494000 sequences read
495000 sequences read
496000 sequences read
497000 sequences read
498000 sequences read
499000 sequences read
500000 sequences read
501000 sequences read
502000 sequences read
503000 sequences read
504000 sequences read
505000 sequences read
506000 sequences read
507000 sequences read
508000 sequences read
509000 sequences read
510000 sequences read
510508 total sequences read
>>STEP 2: READING NODES.DMP FILE
0 nodes read
1000 nodes read
2000 nodes read
3000 nodes read
4000 nodes read
5000 nodes read
6000 nodes read
7000 nodes read
8000 nodes read
9000 nodes read
10000 nodes read
11000 nodes read
12000 nodes read
12923 total nodes read
>>STEP 3: CONVERTING KMER MAPPINGS INTO READ CLASSIFICATIONS:
1000mers, with a database built using 35mers
Time Elaped: 1 minutes, 41 seconds, 0.00000 microseconds
=============================
PROGRAM START TIME: 01-12-2026 11:55:21
...11173 total genomes read from kraken output file
...creating kmer counts file -- lists the number of kmers of each classification per genome
...creating kmer distribution file -- lists genomes and kmer counts contributing to each genome
PROGRAM END TIME: 01-12-2026 11:55:21
Finished creating database1000mers.kraken and database1000mers.kmer_distrib [in DB folder]
*NOTE: to create read distribution files for multiple read lengths,
rerun this script specifying the same database but a different read length
Bracken build complete.
Command error:
510474 sequences converted (finished: LAYC01000003.3856081.3857875)
510475 sequences converted (finished: LKCM01000080.3673.5139)
510476 sequences converted (finished: LASS02003325.4070.5829)
510477 sequences converted (finished: LKUO01000978.8556.10127)
510478 sequences converted (finished: LKUO01003660.7536.9273)
510479 sequences converted (finished: LKUO01003983.25739.27486)
510480 sequences converted (finished: LKUO01004252.6799.8575)
510481 sequences converted (finished: LKUO01004410.7759.9532)
510482 sequences converted (finished: LKUO01004768.11583.13337)
510483 sequences converted (finished: LKUO01004890.22932.24655)
510484 sequences converted (finished: LKUO01005274.897.2663)
510485 sequences converted (finished: LKUO01005140.3744.5530)
510486 sequences converted (finished: LKUO01005616.1.1515)
510487 sequences converted (finished: LKMJ01012234.3184.4646)
510488 sequences converted (finished: LKUO01005795.13826.15972)
510489 sequences converted (finished: LKLZ01000003.1585553.1586832)
510490 sequences converted (finished: LKHX01005117.37952.39807)
510491 sequences converted (finished: LKHY01004835.24824.26669)
510492 sequences converted (finished: LUUB01000105.358.1856)
510493 sequences converted (finished: LUVW01000002.45778.47642)
510494 sequences converted (finished: JOCQ01000207.3420.4908)
510495 sequences converted (finished: JOIY01000094.204.1673)
510496 sequences converted (finished: JOMH01000001.1092401.1093910)
510497 sequences converted (finished: MHEE01000002.15960.17497)
510498 sequences converted (finished: MHYR01000121.4583.6167)
510499 sequences converted (finished: CFFF01000203.442.2194)
510500 sequences converted (finished: JENB01000091.335.1842)
510501 sequences converted (finished: CXYW01000009.360.1734)
510502 sequences converted (finished: CXWL01024289.1436.2731)
510503 sequences converted (finished: CXWK01001735.4041.5385)
510504 sequences converted (finished: MVBC01000034.3.1520)
510505 sequences converted (finished: JQIO01000430.1097739.1099039)
510506 sequences converted (finished: JQHZ01065714.557.1975)
510507 sequences converted (finished: KY979510.1.1479)
510508 sequences converted (finished: )
510509 sequences converted (finished: JQIN01002109.43002.44826)
510511 sequences converted
Time Elaped: 1 minutes, 41 seconds, 0.00000 microseconds
=============================
PROGRAM START TIME: 01-12-2026 11:55:21
...11173 total genomes read from kraken output file
...creating kmer counts file -- lists the number of kmers of each classification per genome
...creating kmer distribution file -- lists genomes and kmer counts contributing to each genome
PROGRAM END TIME: 01-12-2026 11:55:21
Finished creating database1000mers.kraken and database1000mers.kmer_distrib [in DB folder]
*NOTE: to create read distribution files for multiple read lengths,
rerun this script specifying the same database but a different read length
Bracken build complete.
mv: cannot overwrite '/home/sarah/store_dir/SILVA_138_1/./database': Directory not empty
Work dir:
/home/sarah/work/bc/3bdc9aeffc86429ff8e477d240da86
Container:
ontresearch/wf-metagenomics:sha1d71a4d15f57a1c32aacdb94cacdeb268205548e
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
-- Check '.nextflow.log' file for detailsApplication activity log entry
Were you able to successfully run the latest version of the workflow with the demo data?
no