Closed shysol4u closed 4 days ago
kdc10
commented
4 days ago How big in your input file? The printout reads as though minimap is actively running successfully. If your server allows it, I'd recommend increasing the thread usage.
Can you try running the small provided example to verify emu is set up correctly? It should complete in a matter of seconds.
shysol4u
commented
4 days ago I realized later, that the data output from 24 barcodes on the PromethION flow cell was too much. Now running with --t 24 fixed the issue. Thanks much for looking into it.
On Thu, Jul 4, 2024 at 8:24 AM kdc10 @.***> wrote:
How big in your input file? The printout reads as though minimap is actively running successfully. If your server allows it, I'd recommend increasing the thread usage.
Can you try running the small provided example to verify emu is set up correctly? It should complete in a matter of seconds.
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Best Shyam Solanki, P.h.D. Assistant Professor - Plant Microbe Interaction| Department of Agronomy, Horticulture & Plant Science 212, Raven Precision Agriculture Center South Dakota State University, Brookings, SD, 57006 Phone: 701-936-1043 Twitter: @shysol4u
shysol4u
commented
4 days ago Update:
We are experiencing an issue with the smooth running of Emu on our cluster. I hope to find help on this.
Emu is installed with the default and RDP databases, each containing two files: species_taxid.fasta and taxonomy.tsv in the ./shared/databases/ directory (emu/rdp). The output is always the same irrespective of the input I give and process runs even after ~15 hours. A single file, filename.fastq_emu_alignments.sam (1.6 MB), in the ./result directory. The process seems to be stuck. Please help!
SLURM: (1 node, 10 cpus/task/node) emu --type map-ont \ --min-abundance 0.0001 \ -i barcode02_combined_reads.fastq \ --db /cm/shared/databases/emu/emu \ --N 50 \ --K 500M \ --output-dir ./results \ --output-basename barcode03_combined_reads \ --keep-files TRUE \ --keep-counts TRUE \ --keep-read-assignments TRUE \ --output-unclassified FALSE \ --threads 3
The error log output is as follows:
CondaError: Run 'conda init' before 'conda deactivate'
[M::mm_idx_gen::1.2671.09] collected minimizers [M::mm_idx_gen::1.5961.48] sorted minimizers [M::main::1.5991.48] loaded/built the index for 49243 target sequence(s) [M::mm_mapopt_update::1.6101.48] mid_occ = 14113 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 49243 [M::mm_idx_stat::1.618*1.48] distinct minimizers: 462637 (45.14% are singletons); average occurrences: 28.757; average spacing: 5.572; total length: 74133434