ComparativeGenomicsToolkit cactus issues

ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs

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issues

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Why it seems lastz works only use one core

#1392 yuanhao0626 closed 6 months ago
2
Running the docker image in Singularity

#1391 desmodus1984 opened 6 months ago
1
The accelerator {'count': 1, 'kind': 'gpu', 'api': 'cuda', 'brand': 'nvidia'} could not be provided (Singularity container )

#1390 aaannaw opened 6 months ago
3
How to keep large AMBIGUOUS contig in pangenome graph

#1389 Han-Cao opened 6 months ago
3
cactus-hal2chains taking a long time

#1388 lpnunez closed 6 months ago
1
boost memory for filter_paf_deletions

#1387 glennhickey closed 6 months ago
0
question about cactus-hal2maf

#1385 Marh32 opened 6 months ago
4
fix broken --restart in cactus-graphmap

#1384 glennhickey closed 6 months ago
0
filter_paf_deletions request insufficient memory

#1383 Han-Cao opened 6 months ago
4
prepare release 2.8.2

#1382 glennhickey closed 6 months ago
0
update taffy to latest master

#1381 glennhickey closed 6 months ago
0
update to toil 6.1

#1380 glennhickey closed 6 months ago
0
Fix bug where odgi squeeze input paths incorrect with --binariesMode docker

#1379 glennhickey closed 6 months ago
0
Cactus-pangenome fails at odgi squeeze when trying to open "nonexistent" file

#1378 briannadon closed 6 months ago
2
Cactus hanging when specifying "--workDir"

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

#1376 evgenyleushkin opened 6 months ago
11
raise RuntimeError("Failed to parse newick tree: %s" % RuntimeError: Failed to parse newick tree

#1375 Cholineborzoi opened 6 months ago
4
Can Cactus be applied to plant genomes?

#1374 Galaxy-228 opened 6 months ago
1
pangenome.vcf.gz seems to report SV coordinates relative to the END, not start, of the variant

#1373 adadiehl closed 6 months ago
2
Contigs dropped silently from output

#1372 MarionPerrier closed 4 months ago
2
fix cactus-preprocess --maskMode option

#1371 glennhickey closed 6 months ago
0
toil bug in preprocess stage?

#1370 AryehMiller closed 7 months ago
4
WGS bigger than phased reference genome on ODGI Viz plot. (How to use phased and unphased WGS for pangenome with Minigraph-cactus?

#1369 Donandrade opened 7 months ago
5
!!!!run failure after 2 weeks

#1368 song984888 opened 7 months ago
2
how to add a new species as outgroup

#1367 Marh32 opened 7 months ago
2
cactus-hal2maf takes a long time to run

#1366 Sanat-Mishra opened 7 months ago
5
Move maxRefNFrac and minLines filters from hal2maf to maf2bigmaf

#1365 glennhickey closed 7 months ago
0
Try to make illegal instruction message more precise

#1364 glennhickey closed 7 months ago
0
Division by zero error when MAPQ is set to 1

#1363 MarionPerrier closed 7 months ago
1
hal2maf don't contain all the base of reference genome

#1362 chun-he-316 closed 7 months ago
4
Job 'cactus_cons' kind-cactus_cons/instance-06ssc_rv v12 is completely failed

#1361 song984888 opened 7 months ago
1
cactus-hal2maf installation issue

#1360 hopehealey opened 7 months ago
1
Rename intermediate minigraph fasta file

#1359 glennhickey closed 7 months ago
0
about reference-free questions

#1358 HFzzzzzzz opened 7 months ago
1
Minigraph-Cactus: Details on the .gfa.fa.gz output file

#1357 VLoegler closed 7 months ago
1
add vcfwave and bcftools norm

#1356 glennhickey closed 7 months ago
0
hal2maf Error: PermissionError: [Errno 13] Permission denied: 'halStats'

#1355 tinaveit opened 7 months ago
3
gaf2unstable - empty GAF records?

#1354 askleppe opened 7 months ago
1
diploid coverage drop-off

#1353 glennhickey opened 7 months ago
0
turn on --doubleMem by default for clusters

#1352 glennhickey closed 5 months ago
1
Fix cactus-hal2maf --binariesMode docker

#1351 glennhickey closed 7 months ago
0
--restart did not fix failed job

#1350 scintilla9 closed 7 months ago
2
hal2maf

#1349 ferninfm closed 7 months ago
1
AVX2 support

#1348 weiranmmm closed 7 months ago
2
update vg to v1.56.0

#1347 glennhickey closed 7 months ago
0
update abpoa to latest master commit

#1346 glennhickey closed 7 months ago
0
update odgi to v0.8.6

#1345 glennhickey closed 7 months ago
0
Boot job memory for taffy coverage and hgLoadMafSummary

#1344 glennhickey closed 7 months ago
0
v2.8.1 GPU failture! help

#1343 song984888 closed 7 months ago
1
Use bigChain.as from kent src

#1342 glennhickey closed 7 months ago
0

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