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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cactus-graphmap-join on cluster: "Failed job accessed files", but file is exists

#1538 gbdnorden opened 4 hours ago
1
When comparing Cactus, the input evolutionary tree (phylogenetic tree) is not very accurate

#1537 helloworldABCD1234 opened 9 hours ago
5
Merge VCF records at the same position together after bcftools norm left shifts them

#1536 glennhickey opened 22 hours ago
0
update to patched vcfwave; let it work with multiallelics

#1535 glennhickey closed 23 hours ago
0
include downloadVCFWave script in binary release

#1534 glennhickey closed 1 day ago
0
Does input.fa need to be masked by repeatmasker?

#1533 GooLey1025 closed 3 days ago
1
Prep release v2.9.3

#1532 glennhickey closed 3 days ago
0
High UID/GID in Cactus Docker Image Causes Failure with Rootless Docker

#1531 Wabanero opened 4 days ago
1
add vcfwave installation as option to BIN-INSTALL instructions

#1530 glennhickey closed 3 days ago
0
Add checks for invalid sequence characters when writing temporary FASTA files

#1529 glennhickey closed 3 days ago
0
Error in filter-paf-deletion with the command 'vg convert' in minigraph-cactus pipeline

#1528 GooLey1025 opened 5 days ago
3
Cactus-pangenome

#1527 omakias closed 3 days ago
3
Update to patched mafTools

#1526 glennhickey closed 4 days ago
0
Crash after weeks with errors about fastas with bad headers and empty fasta sequences

#1525 mtvector opened 6 days ago
7
tighten disk usage estimate for tile_alignments

#1524 glennhickey closed 6 days ago
0
cactus vs multiz

#1523 evgenyleushkin opened 1 week ago
1
cactus-hal2maf issue at taffy norm ?

#1522 jeramiahsmith closed 4 days ago
8
hal to multiple sequence fasta alignment

#1521 dylandebaun opened 1 week ago
1
Question about gap deletions, gap ins and gap dups

#1520 lsoler-clavel opened 2 weeks ago
1
cactus-hal2chains keep the best match

#1519 lyt57 opened 2 weeks ago
2
apply local TMPDIR redirect to all singularity commands

#1518 glennhickey closed 2 weeks ago
0
set bcftools sort tempdir

#1517 glennhickey closed 2 weeks ago
0
error with mutifurcation

#1516 matdechiara closed 2 weeks ago
1
make --maxLen default in cactus-align consistent with cactus-pangenome

#1515 glennhickey closed 2 weeks ago
0
Sort flowers by total-base-length instead of cap-number for bar/ref

#1514 glennhickey closed 2 weeks ago
0
update to latest vcflib

#1513 glennhickey closed 3 weeks ago
2
Minimal configuration for 100 genomes mammal size

#1512 fgualdr opened 3 weeks ago
4
[experimental] option to estimate alignment score parameters from input pangenome data

#1511 glennhickey closed 1 week ago
0
Retrieving Regions from Alignment

#1510 Tinydxy closed 3 weeks ago
1
Only use abPOA's progressive mode if input lengths all (about) the same

#1509 glennhickey closed 4 weeks ago
0
Question about pangenome building in species with high level of large translocations

#1508 GabrieleRigano99 opened 4 weeks ago
2
Small hacks to maybe avoid potential pangenome race condition

#1507 glennhickey closed 4 weeks ago
0
switch to patched vg to fix paths -n

#1506 glennhickey closed 4 weeks ago
0
exit_status 120

#1505 minglibio closed 2 weeks ago
1
slurm erro

#1504 jwli-code opened 1 month ago
1
update odgi to latest release v0.9.0

#1503 glennhickey closed 1 month ago
0
Inquiry Regarding Minigraph-Cactus v2.9.1 Pipeline for Rare Genetic Disease Analysis

#1502 jinhua2024 closed 1 month ago
0
prep release v2.9.2

#1501 glennhickey closed 1 month ago
0
add --collapse to yeast test

#1500 glennhickey closed 1 month ago
0
unable to write rGFA tags for path

#1499 jinhua2024 closed 1 month ago
3
fix (merge?) bug in collapse logic

#1498 glennhickey closed 1 month ago
0
use exact disk estaimte for merge_alignments job

#1497 glennhickey closed 1 month ago
0
Identifying orthologous sites

#1496 Marh32 opened 1 month ago
4
How does cactus run on multiple nodes in a cluster？

#1495 jwli-code closed 1 month ago
1
Job used more disk than requested.

#1494 jeramiahsmith opened 1 month ago
4
Duplicated variants in a pangenome VCF

#1493 Han-Cao opened 1 month ago
10
v2.8.1: diploid input, haploid output

#1492 dmjask opened 1 month ago
3
Refactor VCF export

#1491 glennhickey closed 15 hours ago
0
VCF output for different "--filter N" option

#1490 shin0727 opened 1 month ago
1
update abpoa to v1.5.3

#1489 glennhickey closed 1 month ago
0