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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Unbound local error

#381 MarnusStoltz closed 4 years ago
4
Step 6 - Fixing threading optimization

#380 isaacovercast opened 4 years ago
0
min_sample_locus and popfile

#379 giorgio-92 closed 4 years ago
2
Merging after step 2 creates `concatedit` file in cwd, which is not ideal.

#378 isaacovercast closed 4 years ago
1
Debugging bioconda

#377 isaacovercast closed 1 year ago
4
denovo+reference/denovo-reference not supported in v0.9 (yet)

#376 leonardslog opened 4 years ago
25
Step 6 KeyError with pops file if sample name not in assembly

#375 isaacovercast closed 4 years ago
5
v0.9 - Step 6 "AssertionError: no consensus files found"

#374 isaacovercast closed 4 years ago
2
i5 demux PCR duplicates

#373 eaton-lab opened 4 years ago
0
insert size hackersonly override

#372 eaton-lab closed 3 years ago
1
baba module not updated to 0.9 version

#371 isaacovercast opened 4 years ago
5
Update documentation

#370 brpark29 closed 4 years ago
2
Exception in step 5: ValueError(All chunk dimensions must be positive (all chunk dimensions must be positive))'

#369 isaacovercast closed 4 years ago
3
Step 3 fails for FASTQ+64 formatted data

#368 isaacovercast closed 3 years ago
5
No loci pass filtered_by_min_sample in step 7

#367 DennisLarsson closed 4 years ago
13
If i want start at the step of 3,how can i generate *.json file ?

#366 lqsae closed 4 years ago
1
Feature Request: sanples with different ploidy levels in same analysis

#365 ClaudiaPaetzold closed 4 years ago
3
Is *_outfiles/tmpdir not getting deleted?

#364 isaacovercast closed 4 years ago
1
total_reads == cut_found?

#363 isaacovercast opened 5 years ago
1
v0.9 - 'jupyter' not coming down as a dependency during bioconda install

#362 isaacovercast closed 5 years ago
1
v0.9 ipa.structure can't currently accept .str/.vcf files from other programs

#361 ksil91 closed 3 years ago
6
Problem when running tetrad : OSError(libmkl_rt.so: cannot open shared object file: No such file or directory)

#360 rancilhac closed 5 years ago
2
v0.9 - Bring back the unlinked output files

#359 isaacovercast closed 5 years ago
1
v0.9 - Filtering stats are wrong in weird ways (max indels)

#358 isaacovercast closed 5 years ago
2
(0.6.27) Step 7 error in introductory tutorial

#357 AlexaDiNicola closed 5 years ago
4
v0.9 - .vcf output uses 9/9 for missing rather than ./.

#356 isaacovercast closed 4 years ago
2
Step 2: Error in cutadapt

#355 caranlove closed 5 years ago
1
v0.9 - API mode fails silently if setting a param that doesn't exist.

#354 isaacovercast closed 3 years ago
2
how to convert python 2 to python 3 when using ipyrad 0.9.12 in jupyter

#353 yexiaying closed 5 years ago
1
Step 4 fails with tuple index error while heterozygosity estimation

#352 eikemq closed 5 years ago
2
Added FastTree to Hotfix

#351 camayal closed 4 years ago
0
v0.9 Step 7 write_loci_and_alleles ValueError

#350 EmilyPhelps closed 5 years ago
18
analysis tools update to toytree 0.2 API

#349 isaacovercast opened 5 years ago
1
dear ipyrad support

#348 huangl07 closed 5 years ago
1
example data for baba analyses

#347 zelongnie closed 5 years ago
1
'module' object has no attribute 'bucky'

#346 yexiaying closed 5 years ago
10
Problem with "Step 3: clustering"

#345 StuntsPT closed 5 years ago
13
Ipyrad issue when using reference genome

#344 mataman2017 closed 5 years ago
3
v0.9 - Write unlinked formats

#343 isaacovercast closed 4 years ago
4
hotfix - Fails to clean up ipcluster in CLI mode

#342 isaacovercast closed 5 years ago
1
step3 error

#341 dxkyq917 closed 5 years ago
1
hotfix - merge forcing project_dir to ./

#340 isaacovercast closed 3 years ago
2
ipyrad Permission denied error

#339 caranlove closed 5 years ago
1
Update ipyrad STRUCTURE notebook with new argument names

#338 ricoperdiz closed 3 years ago
1
dfoil analyses with ipyrad

#337 jferrerobiol closed 5 years ago
1
Docs - release notes not getting updated on rtft

#336 isaacovercast closed 4 years ago
2
Step 7 error

#335 ghost closed 4 years ago
11
ipcluster badly killed

#334 JeremyLGauthier closed 5 years ago
1
0.9.0 - ipcluster not being cleaned up

#333 isaacovercast closed 5 years ago
3
0.9.0 - detect_cpus() is wonky

#332 isaacovercast closed 5 years ago
4

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