conversiontag-IndexError

[dimbots]

Hello,

I am running the NASC-seq pipeline and I am experiencing and error during the conversiontag.

After the annotate step, i am getting the annotated_sorted bam file.
Below are the first 10 lines
bam.txt

I have also created a strandedness.csv file with strandednesFilePreparation.R
(first 10 lines)
strandedness.csv

Even though the tagged bam file is created
bam_tagged.txt

I am getting this error when I run the conversiontag step.
log.error.conversiontag.txt

I suppose that a PosTag.csv file should be created here also, but it is not.

The gtf file I am using looks like this (in case it matters)
gtf.txt

Do you have any idea what could be the problem?
Thanks

[AntonJMLarsson]

Hello,

I think we have figured out why this happens and implemented a fix. Try pulling the fix and run it again.

Best,
Anton

[dimbots]

Hi Anton,
Thank you very much for your prompt reply.

Could you please let me know if you have pushed the fix into the repository? I am asking you because I haven't seen
any changes to the code and even if I git clone again the repository there is the same result and error that I am getting while running the pipeline.
All code text is the same and last visible change was 2 years ago.

Best,
Dimitris

[AntonJMLarsson]

Hi,

The change should be in the repository now, please pull again.

Best,
Anton

[dimbots]

Hi,
I have run it with the fix and now I am having this error.
error.txt

Best,
Dimitris

[dimbots]

Hello,
Do you have any update on this?
Thank you,
Dimitris