Stuck on prep stage

[alicegodden]

Hello,

I've run deviaTE and get stuck at the point of generation of .sam file. The script doesn't stop, and no errors are generated or anything in the log files.
I was wondering if it had anything to do with my fasta file. Do you have any advice on how to generate the TE fasta file for this pipeline please?

This is an example of how my file looks for Danio rerio GRCz11-
DNA|CMC-EnSpm|EnSpm-4N1_DR|EnSpm-4N1_DR_copy1||1|4190-4331 AATAATCTCAG....

This is the script I'm executing-
deviaTE --input_fq sample.fastq.gz --families DNA --library tes_devia.fasta --read_type phred+33

Or do you think it could it be an issue with my conda environment?
Thanks,
Alice

[W-L]

Hi Alice,
Thanks for your message. If the program starts as expected I don't think it would be an issue with the conda environment or other aspects of the setup. The sample of the fasta file you shared does not look like a regulary-formatted fasta file though. It might have been caused by github formatting your message, but fasta files should look more like:

>header1
ACGTACGT...
>header2
ACGTACGT...
...

Would you mind checking your file again?
Lukas

[alicegodden]

Hello, Thank you for your email. I’ve also tried with a fasta file that looks like this, and as you describe It generates the trimmed file, then the sam file, but seems to get stuck indefinitely, and does not write anything to the logs. Any advice would be greatly appreciated. Many thanks Hi Alice, Thanks for your message. If the program starts as expected I don't think it would be an issue with the conda environment or other aspects of the setup. The sample of the fasta file you shared does not look like a regulary-formatted fasta file though. It might have been caused by github formatting your message, but fasta files should look more like:

header1

ACGTACGT...

header2

ACGTACGT... ... Would you mind checking your file again? Lukas — Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BAQKYL2SYYDGSUI7WKFEM3DYRS7JVAVCNFSM6AAAAABCWKXCY2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRTGU2DCMZYGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[W-L]

Thanks!
One thing you could try is to deactivate the detection of internally deleted TEs. That is, if you are not specifically interested in them. You can turn off this feature by running deviaTE with --no_delet_detect. This deactivate one of the more complex parts of the code and should speed up the analysis.
Please let me know if this helps