Empty file umi12.fa with test data R9.41

[vincentmerckx]

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]

Hi Vincent,

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

regards
Søren

[vincentmerckx]

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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFL2E4V7AZVDFSV3DH3SZOTULLHFVANCNFSM4ZCKOI6Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Dr. Vincent S.F.T. Merckx Group leader of *Understanding Evolution*, Naturalis Biodiversity Center, Leiden, the Netherlands Associate Professor, Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands ***@***.*** | +31 6 23315925

[marsfro]

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