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Cannot run my dataset using the pipeline #4

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newuser1971 opened this issue Jun 21, 2023 · 9 comments
Open

Cannot run my dataset using the pipeline #4

newuser1971 opened this issue Jun 21, 2023 · 9 comments

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@newuser1971
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I installed the pipeline on centos 7 cluster. I can run the pipeline using test_data successfully. When I tried to run my own dataset, the pipeline failed. The workflow terminated earlier.

image
@jinfinance
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Thank you for trying out our pipeline!

Based on the screenshot provided, it appears that you are running the pipeline with your own dataset, albeit with the test profile setting, which is fine. I noticed that each process is tagged with "3-AdVB3-27_no_human," indicating that you have already updated the 'params.reads' parameter to point to your data path, and there is only one fastq.gz file in that folder. However, it's important to confirm whether you have also created your own primer information file and updated the 'params.primer' parameter accordingly. If not, the pipeline will use the given '451_subset_primer_pairs' for the primer removal step.

Regarding the issue you mentioned, it would be helpful to know if any errors were thrown by Nextflow or if the pipeline terminated abruptly without any warning.

If you are willing to share your '3-AdVB3-27_no_human' reads file and your primer information file, we would be happy to test them on our end. This will assist us in further investigating the problem.

Thank you.

@newuser1971
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newuser1971 commented Jun 22, 2023 via email

@jinfinance
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Thank you Haibin,

But I only saw the primer info attached to the end of your message. There are no attachment files.. Maybe you can push them to one of your github repos and forward me the link.

@jinfinance
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a few more thoughts. If it the pipeline did terminate without any warnings, it seems like either pair_merging process or quality_filtering process did not generate any outputs, so all subsequent processes just stopped (because there are no inputs).

Can you check that in the pipeline's output folder, there should be a '3-AdVB3-27_no_human' folder with a 'temp' sub-folder in there. And there should be some fastq files in the 'temp' folder.

One more thing, I actually don't know much about primers, but your primer length appears to be very long, 48 bps ?

@newuser1971
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I checked the work/ directory in the first step "cutadapt" there are 28 fastq files whose size are all zero so I think it is not successful in the first step.

Yes the primer is long.

@newuser1971
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I attached the files below:
Thank you!

3-AdVB3-27_no_human_R1.fastq.gz
3-AdVB3-27_no_human_R2.fastq.gz
Juno_Justin_Primer_Pairs.txt
nextflow.log
nextflow.config.txt

@jinfinance
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Sorry for the late response. I was on the road for a week. Thanks for all uploading all the files, I will try them out and let you know what I may find out.

@newuser1971
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newuser1971 commented Jul 6, 2023 via email

@newuser1971
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Do you guys have any update on this issue?

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@newuser1971 @jinfinance