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SorenKarst / longread_umi

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Empty file umi12.fa with test data R9.41 #43

Open vincentmerckx opened 3 years ago

vincentmerckx commented 3 years ago

Hi Soren,

I'm really enthusiastic about the approach you developed! However, I recently tried to run the longread_umi pipeline on my own ONT data and got stuck. To see how the pipeline should behave, I tried running the R9.4.1 test data, but this gave the same error.

Running the script with the R9.4.1 test data I get the following error (Line 327; see full log attached):

---Fatal error--- Empty file test_r941/umi_binning/umi_ref/umi12f.fa

So something goes wrong in the umi_binning part of the script, I guess when extracting UMI pairs with correct lengths, because the resulting file (umi12.fa) is empty. Any idea what is wrong?

Thanks for your feedback!

Vincent

longread_umi_nanopore_pipeline_log_2021-03-04-20:15:25_issue.txt

SorenKarst commented 2 years ago

Hi Vincent,

Sorry about this. This looks weird. Did you figure out what was going on?

regards Søren

vincentmerckx commented 2 years ago

Hi Søren,

Thanks for getting in touch. No, unfortunately I never got past this issue, not with my own data nor with the example data. And I really don't know what goes wrong.

Cheers,

Vincent

Op wo 10 nov. 2021 om 21:15 schreef SorenKarst @.***>:

Hi Vincent,

Sorry about this. This looks weird. Did you figure out what was going on?

regards Søren

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marsfro commented 1 year ago

Hi Soren,

I'm really enthusiastic about the approach you developed! However, I recently tried to run the longread_umi pipeline on my own ONT data and got stuck. To see how the pipeline should behave, I tried running the R9.4.1 test data, but this gave the same error.

Running the script with the R9.4.1 test data I get the following error (Line 327; see full log attached):

---Fatal error--- Empty file test_r941/umi_binning/umi_ref/umi12f.fa

So something goes wrong in the umi_binning part of the script, I guess when extracting UMI pairs with correct lengths, because the resulting file (umi12.fa) is empty. Any idea what is wrong?

Thanks for your feedback!

Vincent

longread_umi_nanopore_pipeline_log_2021-03-04-20:15:25_issue.txt Hi Vincent! Did you solve this problem? I have the same. Thank you, Maria