Recent changes to support-requests

#1 mummer and/or mgaps returned non-zero

TATIANA — Wed, 26 Jan 2022 02:53:00 -0000

I got a mummer error.
I ran mummer for two weeks, and it crashed due to low memory last night. One chromosome was left to be processed.
Is it possible to run the mummer only on the remaining chromosome and combine the outputs?

[MUMMER/4.0.0beta2] nucmer4 --genome option and segmentation fault

Fernando Cruz — Tue, 21 Jul 2020 07:40:36 -0000

Dear Aleksey and Steven,

I have tried to run nucmer4 to compare a contiguous bird genome assembly against the chicken chromosomes (discarding the one with MHC in it). In order to do so I am just running nucmer with defaults and the --genome option and 24 threads (1TB). However I am getting an error saying segmentation fault:

cat test_nucmer4_module.log
remove PYTHON/2.7.5 (PATH)
remove jip-2.7/0.6 (PATH)
load GNUPLOT/5.2.7 (PATH)
load gcc/6.3.0 (PATH, MANPATH, LD_LIBRARY_PATH)
load PERL/5.22.1 (PATH, MANPATH, LD_LIBRARY_PATH)
load MUMMER/4.0.0beta2 (PATH)
running nucmer4 with genome option for large queries
./run_module_mummer4.0.0beta2.sh: line 29: 31318 Segmentation fault nucmer -t 24 --genome -p PavCri9_vs_Chicken_genome Gallus_gallus.chromNames.noChromMT.fa PavCri9.fa

real 15m2.108s
user 19m21.686s
sys 0m11.489s

running mummerplot with defaults on PavCri9_vs_Chicken_genome.delta

gnuplot 5.2 patchlevel 7
ERROR: Could not read PavCri9_vs_Chicken_genome.delta, File is empty

real 0m0.603s
user 0m0.062s
sys 0m0.026s

sed -n 29,29p evaluations/PavCri9/mummer4/run_module_mummer4.0.0beta2.sh
time nucmer -t 24 --genome -p PavCri9_vs_Chicken_genome Gallus_gallus.chromNames.noChromMT.fa PavCri9.fa

Note that, this is a fresh installation done by IT. The previpous one I installed myself and without the --genome option results were weird (single-dot alignments). With --genome option I´ve got same results as above.

Do you have any idea of how to fix this issue? Is there any new developmental version that we could test in our SLURM cluster? We are really insterested in assembling large genome assemblies for evaluation purposes or SV detection.

Thanks in advance,
Fernando

nucmer - postnuc hang on step 4 FINISHING DATA

Milo — Fri, 21 Nov 2014 01:20:26 -0000

!!! 2014-11-04 13:18:13 Running: /root/Downloads/MUMmer3.23/nucmer -maxmatch -c 40 all-gjcombs.ref.seq all-gjcombs.qry.seq -p all-gjcombs
1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
reading input file "all-gjcombs.ntref" of length 1065681070
construct suffix tree for sequence of length 1065681070
(maximum reference length is 2305843009213693948)
(maximum query length is 18446744073709551615)
process 10656810 characters per dot
....................................................................................................
CONSTRUCTIONTIME /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 1055.62
reading input file "/raid/MultiK_Assembly/gerjamdata/all-gjcombs.qry.seq" of length 1065681069
matching query-file "/raid/MultiK_Assembly/gerjamdata/all-gjcombs.qry.seq"
against subject-file "all-gjcombs.ntref"
COMPLETETIME /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 11556.20
SPACE /root/Downloads/MUMmer3.23/mummer all-gjcombs.ntref 2086.07
4: FINISHING DATA

mummer and/or mgaps returned non-zero

Anonymous — Wed, 02 Nov 2011 18:53:50 -0000

1: PREPARING DATA
2,3: RUNNING mummer AND CREATING CLUSTERS
# reading input file "out.ntref" of length 479987453
# construct suffix tree for sequence of length 479987453
# (maximum reference length is 536870908)
# (maximum query length is 4294967295)
# process 4799874 characters per dot
#................................................................................ERROR: mummer and/or mgaps returned non-z
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