nggvs
commented
1 year ago Hi! Thank you for using the workflow! It may be something related with your data. Could you send me the next files so that I can investigate what is happening.
In the EPI2ME Desktop application go to "Track Analyses" (in the dashboard), choose the one that has been "stopped with Error" and click on "Open folder", then move to the directory:work/9a/b9812e3a3d4426f3e6a1e5644776c1. It should be a folder called 'lineages'
Could you send me the content of that folder? You can zip it to send it through GitHub
EsbergA
marsfro
Operating System
macOS
Other Linux
No response
Workflow Version
wf-metagenomic v2.5.0
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
No response
CLI command run
{ classifier: minimap2, batch_size: 0, analyse_unclassified: false, watch_path: false, database_set: ncbi_16s_18s, store_dir: store_dir, taxonomic_rank: S, port: 8080, host: localhost, external_kraken2: false, kraken2_memory_mapping: false, include_kraken2_assignments: false, kraken2_confidence: 0, minimap2exclude: false, split_prefix: false, keep_bam: false, amr: false, amr_db: resfinder, amr_minid: 80, amr_mincov: 80, abundance_threshold: 0, n_taxa_barplot: 8, out_dir: /Users/andersesberg/epi2melabs/instances/wf-metagenomics_01HAVTWSBWFR1X79WYJS52TPA3/output, min_len: 1200, threads: 4, server_threads: 4, kraken_clients: 2, disable_ping: false, help: false, version: false, fastq: /Users/andersesberg/epi2melabs/demo/epi2me-labs/wf-metagenomics/wf-metagenomics-demo/Lime9, min_read_qual: 12, max_len: 1700, wf: { agent: epi2melabs/5.1.2, epi2me_instance: 01HAVTWSBWFR1X79WYJS52TPA3, epi2me_user: guest_01HA9A2WRWMYV0YYDJJ20STRSX } }
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
Run stopped with error in the minimap report step, all other step worked This happens with 2 out of 9 run. Tried to re-run but this does not help. Best regards Anders
Relevant log output
Application activity log entry
No response