Recycler

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RuntimeWarning: invalid value encountered in sqrt

5

This warning occurs for some of my files but not all. **~/anaconda3/lib/python3.6/site-packages/recycler-0.62-py3.6.egg/recyclelib/utils.py:178: RuntimeWarning: invalid value encountered in sqrt** after I issue the recycle.py command, It will run through several "#...

Freemacl

No output produced

3

I have got the recent pull of Recycler installed. The contigs/scaffolds were produced by SPAdes-3.11.1. The kmer size etc were all under 55 etc. Recycler is NOT generating any outputs....

sum732

I thought it would be useful (for debugging purposes, for example) to add date and time to the recycler.py script. Thus, i added to my local recycler.py, on line 194...

greytear

Hello Is there any chance to add support for GFA graph format? Currently as I understand Recycler only works with FASTG format New tools like Unicycler (basically a Spades assembler...

VadimDu

ImportError: No module named recyclelib.utils

1

I recently had to reinstall pysam (using conda) and now Recycler is not working for some reason... Here is what I am trying to run in the terminal: Recycler/bin/recycle.py -g...

gamer3051

mapping input contig names to output

6

Given that I get a contig name like `RNODE_1_length_2185_cov_1230.39000`, how would I know which contig that is in the original file? I can search the coverage field `1230.39` to find...

lskatz

error after running recycle.py

8

recycle.py -g assembly_graph.fastg -k 55 -b reads_pe_primary.sort.bam I got the below erro Traceback (most recent call last): File "/home/omnah486/miniconda2/bin/recycle.py", line 4, in __import__('pkg_resources').run_script('recycler==0.6', 'recycle.py') File "/home/omnah486/miniconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 744, in run_script...

OAF12

error creating the BAM file

1

Hi I'm trying to create the BAM file and it gives an error. I have installed recycler using bioconda. This is the error: Danielas-Mac:Recycler niazevedo$ make_fasta_from_fastg.py -g assembly_graph1.fastg Traceback (most...

Niazevedo

best assembler for the job?

1

Hi, I was wondering what assembler the authors recommend before running Recycler. It seems like spades is recommended, but then I was also wondering what parameters you would recommend. Is...

lskatz