Open buchanri opened 2 months ago
I installed nextflow and the latest version of the pipeline. I wanted to test it first on one of the test datasets but I got an error. I was wondering if this is a issue with the pipeline or just the test dataset I used?
Input: nextflow run main.nf --sample_data https://raw.githubusercontent.com/grunwaldlab/pathogensurveillance/master/test/data/metadata/xanthomonas_small.csv --out_dir /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/test/data/xan_small --download_bakta_db true -profile mamba --max_memory 200.GB --max_time 240.h --email_on_fail buchanri@oregonstate.edu --max_cpus 32 -resume --temp_dir /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/tmp
Output:
ERROR ~ Error executing process > 'PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:BAKTA_BAKTA (22_335)' Caused by: Process `PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:BAKTA_BAKTA (22_335)` terminated with an error exit status (1) Command executed: bakta \ 22_335_filtered.fasta \ --force --skip-plot --skip-crispr \ --threads 8 \ --prefix 22_335 \ \ \ --db db-light cat <<-END_VERSIONS > versions.yml "PATHOGENSURVEILLANCE:GENOME_ASSEMBLY:BAKTA_BAKTA": bakta: $(echo $(bakta --version) 2>&1 | cut -f '2' -d ' ') END_VERSIONS Command exit status: 1 Command output: parse genome sequences... imported: 241 filtered & revised: 241 contigs: 241 start annotation... predict tRNAs... found: 1 predict tmRNAs... found: 0 predict rRNAs... found: 0 predict ncRNAs... found: 1 predict ncRNA regions... found: 0 skip CRISPR array prediction... predict & annotate CDSs... predicted: 66 discarded spurious: 0 revised translational exceptions: 0 detected IPSs: 0 Command error: /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/conda/bakta_bakta-49113c86da635f9641eee48fb966e3b9/lib/python3.10/site-packages/bakta/features/cds.py:43: UserWarning: sequence should be at least 100000 characters (88372 found) trainings_info = orffinder.train(*seqs, translation_table=cfg.translation_table) parse genome sequences... imported: 241 filtered & revised: 241 contigs: 241 start annotation... predict tRNAs... found: 1 predict tmRNAs... found: 0 predict rRNAs... found: 0 predict ncRNAs... found: 1 predict ncRNA regions... found: 0 skip CRISPR array prediction... predict & annotate CDSs... predicted: 66 discarded spurious: 0 revised translational exceptions: 0 detected IPSs: 0 Traceback (most recent call last): File "/nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/conda/bakta_bakta-49113c86da635f9641eee48fb966e3b9/bin/bakta", line 11, in <module> sys.exit(main()) File "/nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/conda/bakta_bakta-49113c86da635f9641eee48fb966e3b9/lib/python3.10/site-packages/bakta/main.py", line 258, in main cdss_pscc, cdss_not_found = pscc.search(cdss_not_found) File "/nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/conda/bakta_bakta-49113c86da635f9641eee48fb966e3b9/lib/python3.10/site-packages/bakta/pscc.py", line 57, in search raise Exception(f'diamond error! error code: {proc.returncode}') Exception: diamond error! error code: -11 Work dir: /nfs7/BPP/Chang_Lab/paradarc/paper1_bra/scripts/pathogensurveillance/work/0f/4d91768653b6517e713a91e466cfcc Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line -- Check '.nextflow.log' file for details -[nf-core/plantpathsurveil] Sent summary e-mail to buchanri@oregonstate.edu (sendmail)- WARN: Access to undefined parameter `outdir` -- Initialise it to a default value eg. `params.outdir = some_value` -[nf-core/plantpathsurveil] Pipeline completed with errors To clean the cache, run the command: nextflow clean cranky_coulomb -f WARN: Killing running tasks (2)
### Relevant files _No response_ ### System information Container: Conda
Description of the bug
I installed nextflow and the latest version of the pipeline. I wanted to test it first on one of the test datasets but I got an error. I was wondering if this is a issue with the pipeline or just the test dataset I used?
Command used and terminal output
Output: