Location of results
/projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results

Brandon has run a python script to remove the last 11 sequences that TSA people complained about.

And in addition, this script also addresses any sequences that are duplicated.

remove_Ns.py

Removed duplicates and wrote them to their own file (Variety_dupes.fa). The new files are located in /projects/tomato_genome/fnb/dataprocessing/TSA-transcriptomeShotgunAssembly/kelsieData/FCS_tools/FCS_GX/tom_runs/fin_results

They follow this pattern (Variety_contaminant3_removed.fa), We should be ready for another submission. Python script is fix_contam3_v2.py and is in same directory

I think this comment is in the wrong task! I'll copy it over to the TSA task.

FCS adaptor keeps dying due to BLAST step using up too much memory. I have gone up to 350gb per run and still running out of memory. Trying to find a way around this.

Checked troubleshooting page on github and found this:

Can FCS-adaptor run on sequencing reads?

FCS-adaptor is developed to operate on assembled genomes and is not intended to replace adaptor trimming on reads. There are various tools for read trimming; tools that are specialized for sequencing technologies may have a more expansive adaptor catalogue relative to FCS-adaptor.

This could be why my jobs are dying no matter how much memory I give them, the tool cant blast the reads.

OK, good to know. Let's stop trying to filter the reads!

R

This ticket can be closed as we now know that these tools are not suitable for large raw reads.