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bactopia / bactopia

A flexible pipeline for complete analysis of bacterial genomes
https://bactopia.github.io
MIT License
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[question] Nanopore only reads analysis skipped CALL_VARIANTS #274

Open llk578496 opened 2 years ago

llk578496 commented 2 years ago

Hi @rpetit3

We just tried to analyze only the Nanaopore reads, but seems it skipped the CALL_VARIANTS part.

May I ask it is possible to include the CALL_VARIANTS analysis in the pipeline with ONT reads only?

executor > local (13) [d9/75f7c6] process > BACTOPIA:GATHER_SAMPLES (B1) [100%] 1 of 1 ✔ [0e/b92a30] process > BACTOPIA:QC_READS (B1) [100%] 1 of 1 ✔ [86/d65ea3] process > BACTOPIA:ASSEMBLE_GENOME (B1) [100%] 1 of 1 ✔ [68/198517] process > BACTOPIA:ASSEMBLY_QC (B1) [100%] 1 of 1 ✔ [3b/4f8c26] process > BACTOPIA:ANNOTATE_GENOME (B1) [100%] 1 of 1 ✔ [42/664d1d] process > BACTOPIA:MINMER_SKETCH (B1) [100%] 1 of 1 ✔ [7e/f483cb] process > BACTOPIA:ANTIMICROBIAL_RESISTANCE (B1) [100%] 1 of 1 ✔ [- ] process > BACTOPIA:ARIBA_ANALYSIS - [f1/78f798] process > BACTOPIA:MINMER_QUERY (B1 - mash-refseq-k21) [100%] 4 of 4 ✔ [- ] process > BACTOPIA:BLAST - [- ] process > BACTOPIA:CALL_VARIANTS - [- ] process > BACTOPIA:MAPPING_QUERY - [49/8268ef] process > BACTOPIA:SEQUENCE_TYPE (B1 - default) [100%] 1 of 1 ✔ [fe/d78d03] process > BACTOPIA:CUSTOM_DUMPSOFTWAREVERSIONS (1) [100%] 1 of 1 ✔

Bactopia Execution Summary
---------------------------
Bactopia Version : 2.0.1
Nextflow Version : 21.10.0
Command Line     : nextflow run /home/gilmansiu3/miniconda3/envs/bactopia//share/bactopia-2.0.x/main.nf -w /mnt/data/Species-specific/VRE/Enterococcus_faecium/TMH/Bactopia-V2.0.0_wd/work/bactopia --ont --SE fastq/batch00001_barcode01_Case00001-21MB424529.pc.fastq.gz --sample B1 --datasets datasets/ --outdir output/ --species 'Enterococcus faecium' -profile docker
Resumed          : false
Completed At     : 2022-01-24T21:23:02.651943+08:00
Duration         : 33m 9s
Success          : true
Exit Code        : 0
Error Report     : -
Launch Dir       : /mnt/data/Species-specific/VRE/Enterococcus_faecium/TMH/Bactopia-V2.0.0_wd

Completed at: 24-Jan-2022 21:23:03 Duration : 33m 9s CPU hours : 1.8 Succeeded : 13

rpetit3 commented 2 years ago

Hi @llk578496 ,

Its definitely possible, I unfortunately have not had the time to test different ONT methods for variant calling.

Do you have any recommendations for calling variants with ONT reads?

Cheers, Robert

llk578496 commented 2 years ago

Clair3 or Medaka+Longshot might be good for haploid variant calling.

rpetit3 commented 2 years ago

Great thank you! I'll test these out and update soon!

rpetit3 commented 2 years ago

@llk578496 do you have a preference over Clair or Medaka+Longshot?

llk578496 commented 2 years ago

I prefer using Clair3 because it is easier.

rpetit3 commented 2 years ago

I was leaning that way as well, thank you for the feedback! I'll work on getting in the next version or two.

llk578496 commented 2 years ago

Call variants in non-diploid organisms (Haploid calling) Hope this tutorial might help!