Your message dated Sun, 05 Dec 2021 16:04:30 +0000
with message-id <e1mtu06-000fv2...@fasolo.debian.org>
and subject line Bug#1000413: fixed in discosnp 1:2.6.1-1
has caused the Debian Bug report #1000413,
regarding discosnp: autopkgtest regression: Segmentation fault
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1000413: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1000413
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: discosnp
Version: 1:2.5.4-1
X-Debbugs-CC: debian...@lists.debian.org
Severity: serious
User: debian...@lists.debian.org
Usertags: regression
Dear maintainer(s),
With a recent upload of discosnp the autopkgtest of discosnp fails in
testing when that autopkgtest is run with the binary packages of
discosnp from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
discosnp from testing 1:2.5.4-1
all others from testing from testing
I copied some of the output at the bottom of this report. As the test
passes in unstable and because of bug #998143 I wonder if the update of
gatb-core wasn't an ABI breakage and should have seen a SONAME bump and
a proper transition. As this package and gatb-core are handled in the
same team, I'll leave you to figure it out. I think you'd want to block
gatb-core from migrating.
Currently this regression is blocking the migration to testing [1]. Can
you please investigate the situation and fix it?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[0] You can see what packages were added from the second line of the log
file quoted below. The migration software adds source package from
unstable to the list if they are needed to install packages from
discosnp/1:2.5.4-1. I.e. due to versioned dependencies or breaks/conflicts.
[1] https://qa.debian.org/excuses.php?package=discosnp
https://ci.debian.net/data/autopkgtest/testing/amd64/d/discosnp/16901493/log.gz
https://ci.debian.net/data/autopkgtest/testing/amd64/d/discosnp/16901493/log.gz
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
tput: No value for $TERM and no -T specified
Running discoSnp++ 2.3.X, in directory /usr with following parameters:
read_sets=fof.txt
prefix=discoRes_k_31_c_3
c=3
C=2147483647
k=31
b=0
d=1
D=100
s=
P=3
p=discoRes
G=
e=
starting date=Mon Nov 22 15:13:02 UTC 2021
############################################################
#################### GRAPH CREATION #######################
############################################################
/usr/bin/dbgh5 -in
fof.txt_discoRes_k_31_c_3_D_100_P_3_b_0_removemeplease -out
discoRes_k_31_c_3 -kmer-size 31 -abundance-min 3 -abundance-max
2147483647 -solidity-kind one -verbose 1 -skip-bcalm -skip-bglue -no-mphf
[DSK: counting kmers ] 0 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 25, 25,
57] MB [DSK: Pass 1/1, Step 1: partitioning ] 0 % elapsed: 0
min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 53,
53, 57] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 %
elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0
min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 26.4 % elapsed: 0 min 1 sec
remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed: 0 min 1
sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed:
0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 %
elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0
min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 26.4 % elapsed: 0 min 1 sec
remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed: 0 min 1
sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed:
0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 %
elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0
min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 26.4 % elapsed: 0 min 1 sec
remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed: 0 min 1
sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 % elapsed:
0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 26.4 %
elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0 min 3 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 26.4 % elapsed: 0 min 1 sec remaining: 0
min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 26.4 % elapsed: 0 min 1 sec
remaining: 0 min 3 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed: 0 min 1
sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed:
0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 %
elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0
min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 53.4 % elapsed: 0 min 1 sec
remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed: 0 min 1
sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed:
0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 %
elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0
min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 53.4 % elapsed: 0 min 1 sec
remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed: 0 min 1
sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed:
0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 %
elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0
min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 53.4 % elapsed: 0 min 1 sec
remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed: 0 min 1
sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86, 86,
847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 % elapsed:
0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 % mem: [ 86,
86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ] 53.4 %
elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu: 102.7 %
mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting kmers ]
53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec cpu:
102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0 min 1 sec
cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 53.4 % elapsed: 0 min 1 sec remaining: 0
min 1 sec cpu: 102.7 % mem: [ 86, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 53.4 % elapsed: 0 min 1 sec
remaining: 0 min 1 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 1 sec remaining: 0
min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 1 sec
remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 1 sec remaining: 0
min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 1 sec
remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 1 sec remaining: 0
min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 1 sec
remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 1 sec remaining: 0
min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 1 sec
remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 1 sec remaining: 0
min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 1 sec
remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 1
sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85, 86,
847] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 % mem: [ 85,
86, 847] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 101.8 %
mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu:
101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec
cpu: 101.8 % mem: [ 85, 86, 847] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 1 sec remaining: 0 min 0
sec cpu: 101.8 % mem: [ 85, 86, 847] MB
[Bloom: read solid kmers ] 0 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29,
847] MB [Bloom: read solid kmers ] 1.89 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29,
29, 847] MB [Bloom: read solid kmers ] 2.84 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [ 29, 29, 847] MB [Bloom: read solid kmers ]
3.78 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 4.73 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 5.68 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 6.62 % elapsed: 0 min 0 sec remaining: 0
min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read
solid kmers ] 7.57 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB
[Bloom: read solid kmers ] 8.51 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29,
847] MB [Bloom: read solid kmers ] 9.46 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29,
29, 847] MB [Bloom: read solid kmers ] 10.4 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [ 29, 29, 847] MB [Bloom: read solid kmers ]
11.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 12.3 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 13.2 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 14.2 % elapsed: 0 min 0 sec remaining: 0
min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read
solid kmers ] 15.1 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB
[Bloom: read solid kmers ] 16.1 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29,
847] MB [Bloom: read solid kmers ] 17 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29,
29, 847] MB [Bloom: read solid kmers ] 18.9 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [ 29, 29, 847] MB [Bloom: read solid kmers ]
19.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 20.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 21.8 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 22.7 % elapsed: 0 min 0 sec remaining: 0
min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read
solid kmers ] 23.7 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB
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sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29,
847] MB [Bloom: read solid kmers ] 25.5 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29,
29, 847] MB [Bloom: read solid kmers ] 26.5 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [ 29, 29, 847] MB [Bloom: read solid kmers ]
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] 28.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 29.3 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 30.3 % elapsed: 0 min 0 sec remaining: 0
min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read
solid kmers ] 31.2 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29, 847] MB
[Bloom: read solid kmers ] 32.2 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29, 29,
847] MB [Bloom: read solid kmers ] 33.1 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 29,
29, 847] MB [Bloom: read solid kmers ] 34.1 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [ 29, 29, 847] MB [Bloom: read solid kmers ]
35 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 36.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 37.8 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [ 29, 29, 847] MB [Bloom: read solid kmers
] 38.8 % elapsed: 0 min 0 sec remaining: 0
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gatb-core-library version
: 1.4.2
git_sha1 : notset
build_date : 2020-12-02/16:09:31
build_system : Linux-4.19.0-12-amd64
build_compiler : /usr/bin/cc (10.2.0)
build_kmer_size : 32 64 96 128
host name
: ci-326-02f58ef6
nb_cores : 2
memory : 7.8
disk_current_dir : 58.8
max_file_nb : 1024
pid : 1888
configuration config
kmer_size
: 31
mini_size : 10
solidity_kind : one
abundance_min : 3
abundance_max : 2147483647
available_space : 60167
estimated_sequence_number : 620
estimated_sequence_volume : 0
estimated_kmers_number : 43400
estimated_kmers_volume : 1
max_disk_space : 58167
max_memory : 5000
nb_passes : 1
nb_partitions : 2
nb_bits_per_kmer : 64
nb_cores : 2
minimizer_type : lexicographic
(kmc2 heuristic)
repartition_type : unordered
nb_cores_per_partition : 1
nb_partitions_in_parallel : 2
nb_cached_items_per_core_per_part : 16777216
nb_banks : 2
system cpu
: -1.0
repartition system
cpu
: 90.0
dsk bank
bank_uri
: fof.txt_discoRes_k_31_c_3_D_100_P_3_b_0_removemeplease
bank_size : 107428
bank_total_nt : 200000
sequences
seq_number : 2000
seq_size_min : 100
seq_size_max : 100
seq_size_mean : 100.0
seq_size_deviation : 0.0
kmers
kmers_nb_valid : 140000
kmers_nb_invalid : 0
stats temp_files
nb_superkmers
: 13324
avg_superk_length : 10.51
minimizer_density : 2.19
histogram
cutoff : 5
nb_ge_cutoff : 1057
ratio_weak_volume : 0.00
first_peak : 154
kmers
solidity_kind : one
thresholds : 3 3
kmers_nb_distinct : 1062
kmers_nb_solid : 1057
kmers_nb_weak : 5
kmers_percent_weak : 0.5
partitions
nb_partitions : 2
nb_items : 1057
part_biggest : 545
part_smallest : 512
part_mean : 528.5
kind
vector : 2
fillsolid_time : 0.005
1.read : 0.003
2.sort : 0.001
3.dump : 0.001
time : 1.113
fill_partitions : 1.101
fill_solid_kmers : 0.012
system cpu
: 100.9
bloom stats
kind
: neighbor
bitsize : 6378
nb_hash : 4
nbits_per_kmer : 6.034370
time : 0.004
build_from_kmers : 0.004
system cpu
: -1.0
debloom stats
kind
: cascading
impl :
DebloomMinimizerAlgorithm
bitsize : 7662
nbits_per_kmer : 7.248817
cfp : 1284
bloom2 : 868
bloom3 : 362
bloom4 : 54
set : 0
nb : 144
time : 0.014
cascading : 0.005
fill_debloom_file : 0.005
finalize_debloom_file : 0.004
system cpu
: 100.0
branching stats
nb_branching
: 8
percentage : 0.8
checksum_branching : c26285a84228c6e7
time build
: 0.008
system cpu
: -1.0
Graph creation time in seconds: 1
rm -rf trashme_1888_dsk_partitions_gatb
############################################################
#################### KISSNP2 MODULE #######################
############################################################
/usr/bin/kissnp2 -in discoRes_k_31_c_3.h5 -out
discoRes_k_31_c_3_D_100_P_3_b_0 -b 0 -l -P 3 -D 100 -T -coverage_file
discoRes_k_31_c_3_cov.h5 -max_ambigous_indel 20 -verbose 1
/usr/bin/run_discoSnp++.sh: line 554: 1930 Segmentation fault
${kissnp2Cmd}
there was a problem with kissnp2
diff: discoRes_k_31_c_3_D_100_P_3_b_0_coherent.fa: No such file or directory
*** Test: FAILURE on diff .fa
autopkgtest [15:13:04]: test run-unit-test
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: discosnp
Source-Version: 1:2.6.1-1
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
discosnp, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1000...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated discosnp package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 05 Dec 2021 16:34:05 +0100
Source: discosnp
Architecture: source
Version: 1:2.6.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1000413
Changes:
discosnp (1:2.6.1-1) unstable; urgency=medium
.
* New upstream version
Closes: #1000413
Checksums-Sha1:
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7d255d532df76241bf55e7cfd5de623220513b00 1390294 discosnp_2.6.1.orig.tar.gz
9c48fa82eb4d87d55cf989f30a03ffb04cf8c01d 22128 discosnp_2.6.1-1.debian.tar.xz
6249d1bf00a2c745ff2c04cbc7f6585bb2ede77f 7971 discosnp_2.6.1-1_amd64.buildinfo
Checksums-Sha256:
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discosnp_2.6.1-1.dsc
65afa7f0991561a1f8d012cd580b9b5e2a602e869eab18616c46b1259f1068a7 1390294
discosnp_2.6.1.orig.tar.gz
d7a80d2fbec36d9ffaeb1cb2bf2996a297d495248fa11b76aef9c6238b89920f 22128
discosnp_2.6.1-1.debian.tar.xz
03a5bf7b6a3b4ea6d3089e7b03642529f70a448aa0041313ebdc6f325af5d88b 7971
discosnp_2.6.1-1_amd64.buildinfo
Files:
fedf493f08e6b7504d7b43e1e393fa7a 2116 science optional discosnp_2.6.1-1.dsc
bf18bd59ff909a10f1d4d06b329ce7af 1390294 science optional
discosnp_2.6.1.orig.tar.gz
dbec18094939984550c6a888806d5634 22128 science optional
discosnp_2.6.1-1.debian.tar.xz
217c9a6bb2f1be69e4d54ff433bb1ddd 7971 science optional
discosnp_2.6.1-1_amd64.buildinfo
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