earl grey complete pipe line - TEstrainer output

[minhasbushra]

Is there a way the output of TEstrainer can be retained while running the complete earlGrey pipeline? .. like the alignments, that we can visualize when running just TEstrainer. There are only a few files in the strainer directory; they are final output files (strained) along with "classify" and "trf" directories. Thanks

[TobyBaril]

The easiest way to do this is likely to add # to the start of lines 166-169 in EarlGrey/scripts/TEstrainer/TEstrainer_for_earlGrey.sh to prevent the removal of temporary files.

@jamesdgalbraith might have a more elegant solution...

[jamesdgalbraith]

Commenting out the lines with hashes like @TobyBaril suggests is the best option, the debug option is specific to the main TEstrainer pipeline.

[manasealoo]

Hello @TobyBaril ,I have been running EarlGrey for sometimes and it does not go beyond this phase.I am using the gitpod environment and getting this error.

/workspace/microsporidiaResults/micsoporidiaMb_EarlGrey/micsoporidiaMb_strainer
Compiling library
cat: TS_micsoporidiaMb-families.fa_6187/trf/micsoporidiaMb-families.fa.satellites: No such file or directory
ERROR: TEstrainer failed to produce a strain file, please check the log file for more information

I am wondering what could be the problem,could you help?

Regards

[TobyBaril]

Hi @manasealoo, this looks like TEstrainer is not able to find any TEs and satellites as a strain file is not produced. What does the -families.fa file look like in *_Database. Also, I can see you are looking at microsporidia, which have very small genomes. There is the potential that not many TE families are detected, and if they are that they are not passing the quality filters in TEstrainer. In this case, there are likely other methods to identify repeats as opposed to a de novo TE detection.

If you could post your log file and the families file it should give us an indication of what is happening.