search

lpantano / seqcluster

small RNA analysis from NGS data
http://seqcluster.readthedocs.io
MIT License
35 stars 17 forks source link

No UMI transform specified, assuming pre-transformed data. #36

Closed jxshi closed 5 years ago

jxshi commented 5 years ago

Hi,

I tried to repeat the small RNA seq pipeline from bcbio-nextgen that you posted (https://github.com/lpantano/seqcluster/tree/master/data/pipeline_example/mirqc) . However, I got the following error message:

No UMI transform specified, assuming pre-transformed data.
No UMI transform was specified, but /data/proj/mirnatest/raw/SRR950876.fastq.gz does not look pre-transformed.

Can you check for me please?

Thanks for your help!

Best regards,

Jianxiang

lpantano commented 5 years ago

Hi,

Can you share the yaml file for that run?

Is this an error or a message?

Does the pipeline get to the end?

Cheers

On Wed, Nov 28, 2018 at 10:47 PM jxshi notifications@github.com wrote:

Hi,

I tried to repeat the small RNA seq pipeline from bcbio-nextgen. However, I got the following error message:

No UMI transform specified, assuming pre-transformed data. No UMI transform was specified, but /data/proj/mirnatest/raw/SRR950876.fastq.gz does not look pre-transformed.

Can you check for me please?

Thanks for your help!

Best regards,

Jianxiang

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/36, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HChO1MLrgz8kGKcx2qflAeSrbwKIks5uz1jpgaJpZM4Y4415 .

jxshi commented 5 years ago

Hi,

I used the template yaml file that you provided here. Minor change was made since I didn't download hg19 data. So I changed genome_build to GRCh37.

I thinks something was wrong because the pipeline stopped after the error message showed up.

I have also tried to turn off umis tools off in the yaml file, and it didn't work.

Can you check further please? Thank you!

lpantano commented 5 years ago

Hi,

Thanks, I will try to reproduce, but I have recently run small RNA pipeline with that config as it is and everything works.

It would be good if you could share the bcbio-nextgen-debug.log file to help me figure it out what is happening.

Thanks

On Thu, Nov 29, 2018 at 11:01 AM jxshi notifications@github.com wrote:

Hi,

I used the template yaml file that you provided here https://github.com/lpantano/seqcluster/blob/master/data/pipeline_example/mirqc/template.yaml . I thinks something is wrong because the pipeline stopped after the error message showed up.

I have also tried to turn off umis tools off in the yaml file, and it didn't work.

Can you check further please? Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/lpantano/seqcluster/issues/36#issuecomment-442888138, or mute the thread https://github.com/notifications/unsubscribe-auth/ABi_HNUBoIAD7FQSLWm37IoHnbUPPxlKks5u0ATmgaJpZM4Y4415 .

lpantano commented 5 years ago

Hi again,

I just pushed a fix, hopefully, that fixes it.

Please update bcbio to latest development and let me know. Sorry about this issue.

Cheers

jxshi commented 5 years ago

Thank you for your timely reply.

It took quite a long time to upgrade bcbio due to my slow internet connection. The small RNA-seq pipeline can now run without specifying umis.

Cheers!

Jianxiang