Hello I am running into an issue with the MultiQC process wh nf-core #bacass

Hello! I am running into an issue with the MultiQC...

Raunak Vijay

09/09/2024, 8:21 PM

Hello! I am running into an issue with the MultiQC process while using version 2.3.1 of the bacass pipeline:

Copy code

Error executing process > 'NFCORE_BACASS:BACASS:MULTIQC_CUSTOM (1)'

Caused by:
  Process `NFCORE_BACASS:BACASS:MULTIQC_CUSTOM` input file name collision -- There are multiple input files for each of the following file names: nanoplot/NanoStats_post_filtering.txt

I have been using this version for several months, but only recently encountered this error for the first time. This is the command I used:

Copy code

nextflow run '<https://github.com/nf-core/bacass>'
		 -name assembly_5446
		 -params-file '<https://api.cloud.seqera.io/ephemeral/7XA_WuHIwWX1OXYBXSIqUA.json>'
		 -with-tower
		 -r 2.3.1
		 -profile docker

I have attached the sample sheet to this message.

5446_samples.csv

Daniel_VM

09/16/2024, 1:53 PM

I'll take a look at it. You can also add your issue to the nf-core/bacass issue repo 🙂 : https://github.com/nf-core/bacass/issues

❤️ 1

Daniel_VM

09/17/2024, 8:28 AM

Hi @Raunak Vijay, I ran a minimal test using the

test_hybrid

profile but was unable to replicate the issue. It appears that in version

-r 2.3.1

, the Nanoplot module generates the nanotstats file as

${prefix}.txt

(where prefix == ID)(See nanoplot module in 2.3.1 ). In this case, the

MULTIQC_CUSTOM

module sotres the file in the work directory like this: 🤔

Copy code

nanoplot/
|_ ERR044595.txt

Could you please share the

.nextflow.log

so we can investigate further? Additionally, it would be helpful if you test this issue in the

-r dev

branch to see if the problem persists. Thanks 🙌

Steph Smith

09/17/2024, 9:20 PM

@Daniel_VM Here is a nextflow.log file from a run where we ran into this issue. Agreed that it the nanoplot module looks like it should be renaming the NanoStats file with the sample prefix correctly, so I’m not sure where this issue is coming from! I just started a test run on the dev branch and I’ll let you know how it turns out.

nf-4THMkRwW3jXzWl.log

Steph Smith

09/17/2024, 10:54 PM

@Daniel_VM Dev branch run was successful and MultiQC report generated with no issues!

Daniel_VM

09/18/2024, 8:28 AM

Awesome! I hope to create the 2.4.0 release by the end of this week, so you can use

-r 2.4.0

in your command. In the meantime,

-r dev

should work. 💪

Steph Smith

09/18/2024, 11:35 AM

Amazing, thanks so much! 🙂

🙌 1

Raunak Vijay

11/21/2024, 1:50 PM

Hi @Daniel_VM. Unfortunately, we have still been running into the “input file name collision” error on the dev branch of the bacass pipeline. We have observed that this error occurs when running multiple samples with hybrid and long-read assemblies, but it does not occur when processing a single sample with either hybrid or long-read assemblies or when running single or multiple samples with short-read assemblies. I have opened a GitHub issue regarding this problem and with some more information: https://github.com/nf-core/bacass/issues/185. Thank you!

Daniel_VM

12/02/2024, 8:46 AM

Hello, I have been trying, but I did not succeed in reproducing the error. sad cowboy

Open in Slack

Previous Next