ComparativeGenomicsToolkit cactus issues

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

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hal2fasta coordinates not matching with input

#1423 danielagarciacobos4 opened 21 hours ago
1
prep release 2.8.4

#1422 glennhickey closed 5 days ago
0
update vcfbub to v0.1.1

#1421 glennhickey closed 5 days ago
0
Long Running Time and High Memory Consumption for `paffy` in `cactus-blast`

#1420 thiagogenez opened 5 days ago
4
Multiple fasta input, single sample in vcf

#1419 dmjask opened 5 days ago
2
create phylogenetic tree with the alignment maf format

#1418 dandanWang2019 opened 6 days ago
7
use bcftools view to sanity check every vcf

#1417 glennhickey closed 1 week ago
0
Cactus-pangenome fails at make_vcf step only on real data

#1416 amsession closed 5 days ago
3
Large variation in run time and data recovery of cactus-hal2maf when switching reference genomes

#1415 emistasis opened 1 week ago
1
Bump gpu docker to ubuntu 22 as Toil 7.0 seems to want Python version > 3.8

#1414 glennhickey closed 1 week ago
1
maybe the "path" do not exist in the gfa ?

#1413 peanut-nu closed 1 week ago
0
prep release 2.8.3

#1412 glennhickey closed 1 week ago
0
How to find halLiftover from cactus install?

#1411 hopehealey closed 1 week ago
1
fix: handle scientific notation in awk output by converting to float …

#1410 thiagogenez closed 2 weeks ago
1
handle scientific notation awk result

#1409 glennhickey closed 2 weeks ago
0
ValueError in redMasking.py due to invalid literal for int() with base 10

#1408 thiagogenez closed 2 weeks ago
2
vcf location problem in Minigraph catus

#1407 jwli-code opened 2 weeks ago
1
raise RuntimeError("{}Command {} exited {}: {}".format(sigill_msg, call, process.returncode, out))

#1406 1321425744zy opened 2 weeks ago
1
Good practice for Reference-Mapped Short Read Genomes?

#1405 dylandebaun opened 2 weeks ago
2
Toilify vcfwave

#1404 glennhickey closed 2 weeks ago
0
catch errors in vcf-bubwave script

#1403 glennhickey closed 2 weeks ago
0
vcf-bubwave does not raise error when it fails

#1402 Han-Cao opened 2 weeks ago
14
Fixed typo in cactus_maf2bigmaf.py

#1401 ofirr closed 3 weeks ago
1
Documentation updates

#1400 glennhickey closed 3 weeks ago
0
Only trim outgroups if there are any

#1399 glennhickey closed 3 weeks ago
1
system-specified memory limit or not？

#1398 peanut-nu closed 1 week ago
4
Question about final gfa files from Minigraph-Cactus

#1397 SimonaSecomandi opened 3 weeks ago
1
Adjusting config.xml to allow multifurcations

#1396 emistasis closed 4 weeks ago
4
RuntimeError: can't start new thread

#1395 scintilla9 closed 4 weeks ago
9
update to toil 7.0

#1394 glennhickey closed 1 month ago
0
update vg to v1.57.0

#1393 glennhickey closed 1 month ago
0
Why it seems lastz works only use one core

#1392 yuanhao0626 closed 1 month ago
2
Running the docker image in Singularity

#1391 desmodus1984 opened 1 month ago
1
The accelerator {'count': 1, 'kind': 'gpu', 'api': 'cuda', 'brand': 'nvidia'} could not be provided (Singularity container )

#1390 aaannaw opened 1 month ago
3
How to keep large AMBIGUOUS contig in pangenome graph

#1389 Han-Cao opened 1 month ago
3
cactus-hal2chains taking a long time

#1388 lpnunez closed 1 month ago
1
boost memory for filter_paf_deletions

#1387 glennhickey closed 1 month ago
0
question about cactus-hal2maf

#1385 Marh32 opened 1 month ago
4
fix broken --restart in cactus-graphmap

#1384 glennhickey closed 1 month ago
0
filter_paf_deletions request insufficient memory

#1383 Han-Cao opened 1 month ago
4
prepare release 2.8.2

#1382 glennhickey closed 1 month ago
0
update taffy to latest master

#1381 glennhickey closed 1 month ago
0
update to toil 6.1

#1380 glennhickey closed 1 month ago
0
Fix bug where odgi squeeze input paths incorrect with --binariesMode docker

#1379 glennhickey closed 1 month ago
0
Cactus-pangenome fails at odgi squeeze when trying to open "nonexistent" file

#1378 briannadon closed 1 month ago
2
Cactus hanging when specifying "--workDir"

#1377 amsession closed 1 week ago
5
cactus-hal2maf conversion skips aligned regions, when --maximumGapLength > 0

#1376 evgenyleushkin opened 1 month ago
11
raise RuntimeError("Failed to parse newick tree: %s" % RuntimeError: Failed to parse newick tree

#1375 Cholineborzoi opened 1 month ago
4
Can Cactus be applied to plant genomes?

#1374 Galaxy-228 opened 1 month ago
1
pangenome.vcf.gz seems to report SV coordinates relative to the END, not start, of the variant

#1373 adadiehl closed 1 month ago
2