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Shamir-Lab / Recycler

This is the codebase for Recycler, described in our manuscript: https://academic.oup.com/bioinformatics/article/33/4/475/2623362, by Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, and Ron Shamir
BSD 3-Clause "New" or "Revised" License
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recycler.py doesn't end (metagenome data) #40

Closed vjoliveira closed 3 years ago

vjoliveira commented 4 years ago

Hi!

I am trying run a metagenome data in Recycler, however the run starts well but never ends (no error is given). I had no problems making the bam file. The terminal looks like this: " ("NODE_280594_length_1837_cov_7.6655_ID_561187'", 'NODE_662693_length_2433_cov_6.4467_ID_1325385', "NODE_1079610_length_163_cov_6.5000_ID_2159219'", 'NODE_11346_length_524_cov_7.3073_ID_22691') before [7.6655, 6.4467, 6.5, 7.3073] after [0.6738814017310526, 0, 0, 0.3156814017310525] 2019-10-04 12:21:56 4 nodes remain in component 2019-10-04 12:21:57 2 nodes remain in component 2019-10-04 12:21:57 3 nodes remain in component 2019-10-04 12:21:57 2 nodes remain in component 2019-10-04 12:21:57 6 nodes remain in component 2019-10-04 12:21:57 15 nodes remain in component"

It ran for 3 days and did not leave this step.

I used Recycle with plasmid data and it went well.

ilkaybuysal commented 3 years ago

I'm having the similar issue so I was wondering if anyone has an answer to this?

dpellow commented 3 years ago

Is it possible that Recycler is just taking a very long time? How big are the input files? Our recommendation is to use our new tool, SCAPP which is supposed to replace Recycler for assembling plasmids in metagenomic samples. SCAPP: https://github.com/Shamir-Lab/SCAPP

ilkaybuysal commented 3 years ago

it's 28,9 MB (28 890 693 bytes), so the usual size for a contig file I would say