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Feel free to open up any BinSanity related issues, suggestions for improvements, etc.
We are actively working to improve the implemenation and welcome any comments.
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Winona Wijaya
2/28/24
ImportError: cannot import name 'GC' from 'Bio.SeqUtils'
Hello! I've been using binsanity since 2021 and I've never had any problems until I re-
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ImportError: cannot import name 'GC' from 'Bio.SeqUtils'
Hello! I've been using binsanity since 2021 and I've never had any problems until I re-
2/28/24
Ekaterine Gabashvili
1/19/24
Binsanity -wf error
I receive an error: Traceback (most recent call last): File '/global/apps/metagenomics/bbmap/lib/
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Binsanity -wf error
I receive an error: Traceback (most recent call last): File '/global/apps/metagenomics/bbmap/lib/
1/19/24
Yasir Bashir
4/6/22
exporting Binsanity results into Anvi'
Hi all, I am using BinSanity to cluster my contigs. After I am done with running BinSanity, it
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exporting Binsanity results into Anvi'
Hi all, I am using BinSanity to cluster my contigs. After I am done with running BinSanity, it
4/6/22
xvaz...@gmail.com
, …
Jéssica Bianca da Silva
5
2/2/22
Binsanity-lc: estimate -C parameter for large dataset
Hi Jéssica, How big is your dataset? How much mem are you requesting? I checked some of our logs and
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Binsanity-lc: estimate -C parameter for large dataset
Hi Jéssica, How big is your dataset? How much mem are you requesting? I checked some of our logs and
2/2/22
Some Kid
,
Elaina Graham
3
5/26/21
Paired-end reads in a single-end read library?
Hello, I am using the workflow from the anvi'o website; I started with their assembly-based
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Paired-end reads in a single-end read library?
Hello, I am using the workflow from the anvi'o website; I started with their assembly-based
5/26/21
Bill Nelson
,
egrah...@gmail.com
9
4/24/21
Very large contig sets
Hi Bill, Wow that's an insane number of bins but excited it got through! Interesting about checkM
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Very large contig sets
Hi Bill, Wow that's an insane number of bins but excited it got through! Interesting about checkM
4/24/21
Bioinformatic Science
,
Elaina Graham
2
3/25/21
Coverage Profile
Hello Julio, You can find that information here: https://github.com/edgraham/BinSanity/wiki/Usage But
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Coverage Profile
Hello Julio, You can find that information here: https://github.com/edgraham/BinSanity/wiki/Usage But
3/25/21
Jaber Abbaszadeh
,
Elaina
2
4/30/20
error with the 'concat' script
Hello Jaber, I have fixed the inconsistent use of tabs issue (A lot of my python2 scripts had this
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error with the 'concat' script
Hello Jaber, I have fixed the inconsistent use of tabs issue (A lot of my python2 scripts had this
4/30/20
biok...@gmail.com
,
Elaina
3
4/16/20
Error with the coverage file
Just another thought but another possibility you can try is providing the full path to your coverage
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Error with the coverage file
Just another thought but another possibility you can try is providing the full path to your coverage
4/16/20
jigyasa arora
,
Elaina
2
4/16/20
BinSanity docker run-error while running "_continuous_distns.py"
Hello, The docke isn't something I implement often but I'll take a look at this ASAP. It may
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BinSanity docker run-error while running "_continuous_distns.py"
Hello, The docke isn't something I implement often but I'll take a look at this ASAP. It may
4/16/20
nikhila...@gmail.com
,
Elaina Graham
4
5/18/19
Memory usage concerns
Hi Nikhil, So in terms of K-means vs affinity propagation, the main reason our program using affinity
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Memory usage concerns
Hi Nikhil, So in terms of K-means vs affinity propagation, the main reason our program using affinity
5/18/19
waove...@gmail.com
, …
Elaina
4
2/8/19
estimate memory usage ?
Hi Will, I apologize for not getting back to you sooner, but this is all great information. I'm
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estimate memory usage ?
Hi Will, I apologize for not getting back to you sooner, but this is all great information. I'm
2/8/19
bostjan...@fe.uni-lj.si
,
egrah...@gmail.com
2
1/3/19
BinSanity-profile under Miniconda/Bioconda
Hello, First check that you have all dependencies. I see you do not list having installed
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BinSanity-profile under Miniconda/Bioconda
Hello, First check that you have all dependencies. I see you do not list having installed
1/3/19
sumavsu...@gmail.com
,
egrah...@gmail.com
2
10/5/18
Binsanit-profile GZIP error -2
This error seems to be indicating that one or more of the files the program is reading are in a
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Binsanit-profile GZIP error -2
This error seems to be indicating that one or more of the files the program is reading are in a
10/5/18
CN
,
edgr...@usc.edu
2
7/31/18
simplify-fasta not found
Thank you for pointing this out, that script is being overlooked when install binsanity via pip. I
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simplify-fasta not found
Thank you for pointing this out, that script is being overlooked when install binsanity via pip. I
7/31/18
liuguoqi...@gmail.com
, …
Alan Wong
10
6/28/18
have many samples how to binning
Thanks Elaina! So say I have 5 samples (S1,S2,S3,S4,S5). First I have to do is to co-assemble them
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have many samples how to binning
Thanks Elaina! So say I have 5 samples (S1,S2,S3,S4,S5). First I have to do is to co-assemble them
6/28/18
Alan Wong
,
Elaina
2
6/28/18
Index out of range error
My initial inclination would be to check if you have properly set the checkM data folders. So once
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Index out of range error
My initial inclination would be to check if you have properly set the checkM data folders. So once
6/28/18
mail2...@gmail.com
,
edgraham
2
3/23/18
IndexError: list index out of range
The newest version of BinSanity shouldn't throw this error. Let me know though it you continue to
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IndexError: list index out of range
The newest version of BinSanity shouldn't throw this error. Let me know though it you continue to
3/23/18
ne...@ualberta.ca
, …
cami...@gmail.com
3
11/30/17
estimating abundance of bins
Great! Thanks, Camilla On Thursday, 30 November 2017 09:20:10 UTC-7, edgraham wrote: Hi Camilla,
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estimating abundance of bins
Great! Thanks, Camilla On Thursday, 30 November 2017 09:20:10 UTC-7, edgraham wrote: Hi Camilla,
11/30/17
math....@gmail.com
,
Elaina Graham
3
10/18/17
Binsanity-profile stuck
Hi Matt, I attempted to replicate this error, does Binsanity-profile fail to produce the `.saf` and `
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Binsanity-profile stuck
Hi Matt, I attempted to replicate this error, does Binsanity-profile fail to produce the `.saf` and `
10/18/17
edgraham
10/9/17
v0.2.6
We released v0.2.6! See the new and improved github wiki for more information!
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v0.2.6
We released v0.2.6! See the new and improved github wiki for more information!
10/9/17
KC soh
,
edgraham
2
9/5/17
bin evaluation
Hello, So the Bin_evaluation script was written to calculate the adjusted rand index, precision, and
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bin evaluation
Hello, So the Bin_evaluation script was written to calculate the adjusted rand index, precision, and
9/5/17
fernand...@gmail.com
,
edgraham
2
8/23/17
Bins from Binsanity-wf
Hello, So this means there are 5 bins. To explain what those mean you have to think about how the
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Bins from Binsanity-wf
Hello, So this means there are 5 bins. To explain what those mean you have to think about how the
8/23/17
helen...@gmail.com
,
edgraham
6
8/19/17
CheckM data file location?
Hi Helen, Glad to hear it is all up and running! Let me know if there is anything else I can help
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CheckM data file location?
Hi Helen, Glad to hear it is all up and running! Let me know if there is anything else I can help
8/19/17
liuguoqi...@gmail.com
8/15/17
I have many samples how to binning?
Hi,Community I'm very interested in your assembly software BinSanity. I have many samples how to
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I have many samples how to binning?
Hi,Community I'm very interested in your assembly software BinSanity. I have many samples how to
8/15/17
edgraham
8/9/17
New things in BinSanity v0.2.5.11
Hi All, I just wanted to give an update on the changes for v0.2.5.11 of BinSanity Binsanity-wf and
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New things in BinSanity v0.2.5.11
Hi All, I just wanted to give an update on the changes for v0.2.5.11 of BinSanity Binsanity-wf and
8/9/17
donova...@gmail.com
,
Elaina Graham
3
8/9/17
binsanity-checkm directory created in current working directory
Hi Donovan, I updated Binsanity-wf and Binsanity-lc with a new flag to make running things in
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binsanity-checkm directory created in current working directory
Hi Donovan, I updated Binsanity-wf and Binsanity-lc with a new flag to make running things in
8/9/17
edgraham
,
low.pres...@gmail.com
2
5/12/17
BinSanity v0.2.5.9
Hi Elaina, Thanks for maintaining the software; highly appreciated! Best, Jeroen On Friday, 5 May
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BinSanity v0.2.5.9
Hi Elaina, Thanks for maintaining the software; highly appreciated! Best, Jeroen On Friday, 5 May
5/12/17
aditya...@gmail.com
,
edgraham
2
5/10/17
Multithreading support?
Hello Aditya, We have yet to explore parallel computting, but because the algorthim it uses is
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Multithreading support?
Hello Aditya, We have yet to explore parallel computting, but because the algorthim it uses is
5/10/17
rlsm...@gmail.com
,
Elaina Graham
2
5/2/17
Error when running Binsanity-wf
Hello, We had some issues with the the last updates to that script I have been trying to work through
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Error when running Binsanity-wf
Hello, We had some issues with the the last updates to that script I have been trying to work through
5/2/17