Closed Rohit-Satyam closed 11 months ago
Hello @Rohit-Satyam
This is certainly odd. What immediately worries me is the name of the samples:
024_barcode31, 1012643340-D_barcode06, 1016083501-D_barcode02, 1018515054-D_barcode05, 1054883101-D_barcode09....etc
This might be causing some unexpected behaviour, but I can't be sure. You could perhaps try running one or two samples with just the fastq folder called barcode01
and barcode02
etc.
The other thing that catches my eye is a shorter read length distribution:
...but as you say coverage looks alright.
Try the the above and let me know how you get on.
Matt
Hi @mattdmem Thanks for your quick reply. I changed the directories names and kept just the barcodes. I also realized that old parameter --medaka_model
has been replaced by --medaka_variant_model
. That should throw warning or error but it doesn't.
Anyways, still all the barcodes fails. Below is the output of the artic pipeline for two samples. Coming to the read lengths, yes the average read length here is less than 350bp that we had in our previously sequenced samples. But any read greater than 75bp read length should be able to align accurately isn't it? We therefore keep the upper limit to 700bp to avoid chimeric reads but use --min_len
100 or 150 . Having said that, I was wondering if you can use Yacrd to remove chimeric reads instead of using a stringent cutoff of 700bp? I came across this tool recently while analyzing another nanopore data so thought it might be a good addition to this pipeline. Just thinking!!
nextflow run epi2me-labs/wf-artic --fastq $PWD/fastq_pass_renamed/ --out_dir wf-articresults_renamed --scheme_version ARTIC/V4.1 --medaka_variant_model r941_min_fast_variant_g507 --pangolin_version latest --update_data true --report_detailed true -profile singularity --min_len 100
Curious!
Can you send me a bam file from the output? You can attach here if it isn’t too big. Please make sure there are no human reads along for the ride.
Thanks
Matt
CONFIDENTIAL
CONFIDENTIAL
From: Rohit Satyam @.> Sent: Tuesday, September 26, 2023 8:09:25 AM To: epi2me-labs/wf-artic @.> Cc: Matt Parker @.>; Mention @.> Subject: Re: [epi2me-labs/wf-artic] Consensus sequences are not produced even after good coverage (Issue #97)
Hi @mattdmemhttps://github.com/mattdmem Thanks for your quick reply. I changed the directories names and kept just the barcodes. I also realized that old parameter --medaka_model has been replaced by --medaka_variant_model. That should throw warning or error but it doesn't.
Anyways, still all the barcodes fails. Below is the output of the artic pipeline for two samples. Coming to the read lengths, yes the average read length here is less than 350bp that we had in our previously sequenced samples. But any read greater than 75bp read length should be able to align accurately isn't it? We therefore keep the upper limit to 700bp to avoid chimeric reads but use --min_len 100 or 150 . Having said that, I was wondering if you can use Yacrdhttps://github.com/natir/yacrd to remove chimeric reads instead of using a stringent cutoff of 700bp? I came across this tool recently while analyzing another nanopore data so thought it might be a good addition to this pipeline. Just thinking!!
wf-artic-report.ziphttps://github.com/epi2me-labs/wf-artic/files/12723864/wf-artic-report.zip
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Hi @mattdmem. I am embarrassed I think I found my own mistake. This time I cloned the repository and ran the latest version as follows and it worked.
nextflow run main.nf --fastq /data/covid_sept2023/fastq_pass --out_dir wf-articresults --scheme_version \
ARTIC/V4.1 --medaka_variant_model r941_min_fast_variant_g507 \
--pangolin_version latest --update_data true -profile singularity --min_len 100 --update_data false -resume
I shouldn't have ignored the following warning:
NOTE: Your local project version looks outdated - a different revision is available in the remote repository [cb0ad4a440]
Launching `https://github.com/epi2me-labs/wf-artic` [special_kalman] DSL2 - revision: a60a1e1e73 [master]
I was under the impression that each time I specify nextflow info epi2me-labs/wf-artic
, the nextflow will fetch the latest version of wf-artic
pipeline from the github, but when I check it, that's not the case
nextflow info epi2me-labs/wf-artic
project name: epi2me-labs/wf-artic
repository : https://github.com/epi2me-labs/wf-artic
local path : /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic
main script : main.nf
description : Workflow for SARS-CoV-2 Network ARTIC analysis.
author : Oxford Nanopore Technologies
revisions :
* master (default)
mindepth
prerelease
schema
v0.0.2 [t]
v0.0.3 [t]
v0.0.4 [t]
v0.0.5 [t]
v0.0.6 [t]
v0.0.7 [t]
v0.1.0 [t]
v0.1.1 [t]
v0.1.2 [t]
v0.1.3 [t]
v0.1.4 [t]
v0.2.0 [t]
v0.2.1 [t]
v0.2.2 [t]
v0.2.3 [t]
v0.3.0 [t]
v0.3.10 [t]
v0.3.11 [t]
v0.3.12 [t]
v0.3.13 [t]
v0.3.14 [t]
v0.3.15 [t]
v0.3.16 [t]
v0.3.18 [t]
v0.3.2 [t]
v0.3.3 [t]
v0.3.4 [t]
v0.3.5 [t]
v0.3.6 [t]
v0.3.7 [t]
v0.3.8 [t]
v0.3.9 [t]
When I check the nextflow.config file at the location /home/subudhak/.nextflow/assets/epi2me-labs/wf-artic
, I realised I was using old version v0.3.18
(Jul 14, 2022). Can you tell me how to ensure that the latest version of wf-artic
pipeline is used without having to clone repo each time? Is there a nextflow argument to do that?
No worries - I am glad you have solved the problem!
nextflow pull
should update the repository on the command line - in the EPI2ME desktop app you can check for updates using the button
Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
0.3.31
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
Workflow Execution - CLI Execution Profile
None
What happened?
The command was executed successfully but all the samples seems to fail in the HTML report and empty variant files are produced.
Relevant log output
wf-artic-report.zip