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Old 04-11-2019, 04:24 AM   #103
Chief_Lazy_Bison
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Location: Ames, IA

Join Date: Dec 2014
Posts: 9
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It is submitted to a SLURM queue via the attached script.

These reads are a collection of concatenated interleaved paired end libraries

The same script worked well on the individual libraries, but I wanted to do an assembly with all of the reads together so I concatenated them all with
Code:
cat *fq.gz > ALL.fq.gz
The command that ends up stalling is this:
Code:
clumpify.sh in=ALL_temp.fq.gz out=ALL.eccc.fq.gz ecc passes=4 reorder

bbmerge plows through these reads with no complaints just prior to clumpify

Code:
bbmerge.sh in=ALL_temp.fq.gz out=ALL.ecco.fq.gz ecco mix vstrict ordered ihist=ALL_ihist_merge1.txt
Attached Files
File Type: txt ALL_ec.SLURM.txt (6.5 KB, 1 views)
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