kalign fail when sequences in input file are almost the same.
Closed this issue · 1 comments
xiekunwhy commented
Hi,
Kalign fail when sequences in input file are almost the same. Would you please fix this bug.
family.zip
Best,
Kun
/Bio/User/kxie/software/mambaforge/envs/kalign3/bin/kalign --nthreads 4 --format fasta --type protein -i /state/partition1/WORK/Bio/Project/xiek/pipe/compareGenomic/BeiChaiHu/pipe3/02.ortholog/04.msa/pep/OG0000001.pep.fa -o /state/partition1/WORK/Bio/Project/xiek/pipe/compareGenomic/BeiChaiHu/pipe3/02.ortholog/04.msa/alnpep/OG0000001.pep.aln
Kalign (3.4.0)
Copyright (C) 2006,2019,2020,2021,2023 Timo Lassmann
This program comes with ABSOLUTELY NO WARRANTY; for details type:
`kalign -showw'.
This is free software, and you are welcome to redistribute it
under certain conditions; consult the COPYING file for details.
Please cite:
Lassmann, Timo.
"Kalign 3: multiple sequence alignment of large data sets."
Bioinformatics (2019)
https://doi.org/10.1093/bioinformatics/btz795
[2024-04-14 20:01:58] : LOG : Detected protein sequences.
[2024-04-14 20:01:58] : WARNING : -------------------------------------------- (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 522)
[2024-04-14 20:01:58] : WARNING : All input sequences have the same length. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 523)
[2024-04-14 20:01:58] : WARNING : BUT there are no gap characters. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 524)
[2024-04-14 20:01:58] : WARNING : (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 525)
[2024-04-14 20:01:58] : WARNING : Unable to determine whether the sequences (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 526)
[2024-04-14 20:01:58] : WARNING : are already aligned. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 527)
[2024-04-14 20:01:58] : WARNING : Kalign will align the sequences. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 528)
[2024-04-14 20:01:58] : WARNING : -------------------------------------------- (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/msa_op.c line 529)
[2024-04-14 20:01:58] : LOG : Read 253 sequences from /state/partition1/WORK/Bio/Project/xiek/pipe/compareGenomic/BeiChaiHu/pipe3/02.ortholog/04.msa/pep/OG0000001.pep.fa.
[2024-04-14 20:01:58] : LOG : CPU Time: 0.00u 00:00:00.00 Elapsed: 00:00:00.00
[2024-04-14 20:01:58] : LOG : Calculating pairwise distances
[2024-04-14 20:01:59] : LOG : CPU Time: 0.24u 00:00:00.24 Elapsed: 00:00:01.00
[2024-04-14 20:01:59] : LOG : Building guide tree.
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:01:59] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
[2024-04-14 20:02:00] : ERROR : Failed. (/opt/conda/conda-bld/kalign3_1702189157882/work/lib/src/bisectingKmeans.c line 506)
Segmentation fault
TimoLassmann commented
Hi Kun,
Thanks for reporting! I fixed this issue in the recent commit.
Best, T