dereneaton ipyrad issues

dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets

http://ipyrad.readthedocs.io

GNU General Public License v3.0

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issues

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No progress in struct.run

#584 Zombiekotze opened 1 day ago
1
ipa.raxml should have a `draw` function

#583 isaacovercast opened 3 weeks ago
0
No Progress in analysis

#582 Zombiekotze closed 3 weeks ago
2
Python integer 69530 out of bounds for uint16

#581 amesclir closed 1 month ago
2
Why is the max heterozygotes parameter default so low?

#580 ottoau closed 2 months ago
8
PCA cookbook is out of date

#579 isaacovercast opened 2 months ago
0
PCA plotting is broken w/ numpy > 2.0

#578 isaacovercast opened 2 months ago
2
Step 3 - Samtools sort exec format error

#577 isaacovercast closed 2 months ago
1
Step 2 why is it trimming R1/R2 ?

#576 isaacovercast opened 2 months ago
0
recommended clust_threshold

#575 Ruiqi-CUB closed 2 months ago
5
Individual loci sequence & alignment files

#574 Ruiqi-CUB closed 3 months ago
5
problem with merging option on command line

#573 jesus-mavarez closed 3 months ago
1
Support for muscle v5

#572 isaacovercast opened 3 months ago
1
Overflow error in step 7 with reference genome

#571 reedjohnkenny closed 3 months ago
1
ipa.pca: Include an optional 'default' group for imap to catch samples not included

#570 isaacovercast opened 3 months ago
0
ipa.pca: Allow to pass in a pops file to populate imap

#569 isaacovercast opened 3 months ago
0
step7 error

#568 Zeroo11 closed 3 months ago
1
Ipyrad running on cluster, but not creating .json file or folders

#567 avculley closed 3 months ago
2
running already demultiplexed sequences

#566 Bunholi closed 4 months ago
1
pair_fastqs.py `get_fastq_tuples_dict_from_paths_list` for SE data returns R1/R2 in sample names

#565 isaacovercast closed 3 months ago
1
ipyrad.analysis cannot be imported as libsodium.23.dylib is missing

#564 AleixPalahi closed 3 months ago
2
ipyrad tries to find assembly file instead of reading parameters file

#563 d-caraballo closed 3 months ago
2
Step3: IndexError: string index out of range

#562 ckiel3 closed 3 months ago
22
step 3 slow

#561 ospfsg closed 3 months ago
4
TypeError while using ipyrad.analysis.popgen

#560 spilornis-ng closed 5 months ago
2
analysis.treemix - toytree v3.0 compatibility

#559 isaacovercast opened 7 months ago
0
ipyrad v.0.9.94/95 frozen at the beggining

#558 ospfsg closed 7 months ago
4
No PE fastq pairs detected based on filenames, assuming SE data

#557 angelicagallegonar closed 4 months ago
10
ipyrad reference assembly: Key error 7372

#556 frsepulveda closed 7 months ago
3
iPyrad CLI tutorials (ABBA/BABA tests, Structure, treemix, etc)

#555 jesus-mavarez closed 7 months ago
1
Hyb-seq data, can be used with ipyrad?

#554 AngieOrtizHerrera closed 7 months ago
12
"1" ("2") instead of "_R1_" ("_R2_) in .fq data files

#553 jesus-mavarez closed 7 months ago
2
problems downloading Pedicularis example data

#552 jesus-mavarez opened 8 months ago
1
ipyrad error step 6: ValueError: cannot copy sequence with size 298 to array axis with dimension 299

#551 IvonedeBem opened 8 months ago
4
Popgen summary statistics fails when using imap

#550 zwuckl closed 8 months ago
3
Structure nreps 10 for k=[2, 3, …] on 16 Core CPU will only use 10 CPUs for each K

#549 kindofausername closed 9 months ago
1
Ipyrad excluding samples during demultiplexing stage

#548 ikb001 closed 9 months ago
5
Merging libraries of different read lengths

#547 spilornis-ng closed 9 months ago
1
combinatorial demultiplexing problem

#546 TomaszSuchan closed 9 months ago
4
UnboundLocalError: local variable 'barcode' referenced before assignment

#545 SerenaCaplins closed 9 months ago
3
Repeated pandas FutureWarning messages

#544 AlexaDiNicola closed 10 months ago
2
VCF output fails

#543 TomaszSuchan closed 10 months ago
2
*.ustr file and other files not generated when using a genome as a reference in the assembly method

#542 aroavaron opened 10 months ago
10
In Step 7: Message: ValueError: not enough values to unpack (expected 2, got 1)

#541 aroavaron opened 10 months ago
5
How to export toyplot.csv in Structure analysis ?

#540 khorikhori closed 9 months ago
5
ipyrad - PE original RAD with reference

#539 ivan06513 closed 10 months ago
1
ipyrad-baba error

#538 tsm-tsm closed 10 months ago
7
step3 error

#537 Kenjicoral closed 12 months ago
3
ipyrad-bucky error in python 3.12

#536 tsm-tsm closed 7 months ago
9
tetrad install in python 3.7

#535 tsm-tsm closed 12 months ago
0