Open jeramiahsmith opened 1 day ago
Which version of cactus are you using?
On Tue, Nov 12, 2024 at 4:40 PM jeramiahsmith @.***> wrote:
I am using cactus-hal2maf and the conversion seems to be failing at the stage where it is running taffy norm commands. I included a snippet of the stderr below, but please let me know if you need more.
[2024-11-12T16:00:53-0500] [MainThread] [I] [toil-rt] Successfully ran hal2maf sal10.hal stdout --refGenome AM --refSequence Mex_chr10 --start 1712000000 --length 500000 --maxBlockLen 10000 --noAncestors in time: 0.20 [2024-11-12T16:00:53-0500] [MainThread] [I] [toil-rt] Successfully ran hal2maf sal10.hal stdout --refGenome AM --refSequence Mex_chr10 --start 1712500000 --length 375843 --maxBlockLen 10000 --noAncestors in time: 0.10 [2024-11-12T16:00:53-0500] [MainThread] [I] [toil-rt] First of 3426 commands in parallel batch: set -eo pipefail && cat salj2_chunk_0.maf | (time -p mafRowOrderer -m - --order-file genome.list) 2> 0.sort.time | (time -p taffy view ) 2> 0.m2t.time | (time -p taffy norm -a sal10.hal -k ) 2> 0.tn.time > salj2_chunk_0.norm.maf && mv salj2_chunk_0.norm.maf salj2_chunk_0.maf [2024-11-12T16:00:53-0500] [MainThread] [I] [toil-rt] 2024-11-12 16:00:53.843772: Running the command: "bash -c set -eo pipefail && cat /scratch/jjsmit3/compar/cactus2/tmpmsk2/toilwf-2d27f925d82e5a9c8caca3fb95810aed/3b7c/job/tmp7bt5mnts/taf_cmds.txt | parallel -j 12 '{}'" [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] Parallel taffy command failed, dumping all stderr [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] taffy: taffy/impl/maf.c:58: maf_read_block: Assertion
alignment->column_number == strlen(row->bases)' failed. [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] /usr/bin/bash: line 1: 4025844 Aborted (core dumped) taffy view [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] real 0.59 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] user 0.05 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] sys 0.00 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] /usr/bin/bash: line 1: 4025843 Segmentation fault (core dumped) mafRowOrderer -m - --order-file genome.list [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] real 0.44 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] user 0.00 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] sys 0.00 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] taffy: taffy/impl/taf.c:128: get_bases: Assertion
strlen(column) == column_length' failed. [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] /usr/bin/bash: line 1: 4025845 Aborted (core dumped) taffy norm -a sal10.hal -k [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] real 0.73 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] user 0.17 [2024-11-12T16:03:31-0500] [MainThread] [E] [toil.statsAndLogging] sys 0.01— Reply to this email directly, view it on GitHub https://github.com/ComparativeGenomicsToolkit/cactus/issues/1522, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAG373V56CJNBDKJKJG3ULD2AJYVDAVCNFSM6AAAAABRVATVJKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGY2TGNBQGMZTIMQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
I'm using cactus-v2.9.0
OK, I asked because I think I've seen this issue before in an older Cactus version that the cause that time has been fixed.
Are you able to share the .hal
file with me so I can reproduce it?
I am using cactus-hal2maf and the conversion seems to be failing at the stage where it is running taffy norm commands. I included a snippet of the stderr below, but please let me know if you need more.