[Debian-med-packaging] Bug#998143: gatb-core breaks discosnp autopkgtest: Segmentation fault
Paul Gevers
elbrus at debian.org
Sat Oct 30 21:57:08 BST 2021
Source: gatb-core, discosnp
Control: found -1 gatb-core/1.4.2+dfsg-7
Control: found -1 discosnp/4.4.4-2
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of gatb-core the autopkgtest of discosnp fails in
testing when that autopkgtest is run with the binary packages of
gatb-core from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
gatb-core from testing 1.4.2+dfsg-7
discosnp from testing 4.4.4-2
all others from testing from testing
I copied some of the output at the bottom of this report.
Currently this regression is blocking the migration of gatb-core to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package?
More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
Paul
[1] https://qa.debian.org/excuses.php?package=gatb-core
https://ci.debian.net/data/autopkgtest/testing/amd64/d/discosnp/16314588/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=Sat Oct 30 11:09:22 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,
58] 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, 58] MB [DSK: Pass 1/1, Step 2: counting kmers ] 2.24 %
elapsed: 0 min 2 sec remaining: 1 min 8 sec cpu: 108.3 %
mem: [1902, 1902, 1902] MB [DSK: Pass 1/1, Step 2: counting kmers ]
2.24 % elapsed: 0 min 2 sec remaining: 1 min 8 sec cpu:
108.3 % mem: [1904, 1904, 1904] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 3.72 % elapsed: 0 min 2 sec remaining: 0 min 41 sec
cpu: 109.6 % mem: [1904, 1904, 1904] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 5.27 % elapsed: 0 min 2 sec remaining: 0
min 28 sec cpu: 109.6 % mem: [1904, 1904, 1904] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 5.27 % elapsed: 0 min 2 sec
remaining: 0 min 28 sec cpu: 109.6 % mem: [1905, 1905, 1905] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 6.52 % elapsed: 0 min 2
sec remaining: 0 min 22 sec cpu: 109.6 % mem: [1909, 1909,
1909] MB [DSK: Pass 1/1, Step 2: counting kmers ] 8 % elapsed:
0 min 2 sec remaining: 0 min 18 sec cpu: 110.8 % mem: [1912,
1912, 1912] MB [DSK: Pass 1/1, Step 2: counting kmers ] 8.81 %
elapsed: 0 min 2 sec remaining: 0 min 16 sec cpu: 111.5 %
mem: [1912, 1912, 1912] MB [DSK: Pass 1/1, Step 2: counting kmers ]
10.1 % elapsed: 0 min 2 sec remaining: 0 min 14 sec cpu:
111.5 % mem: [1913, 1913, 1913] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 10.1 % elapsed: 0 min 2 sec remaining: 0 min 14 sec
cpu: 111.5 % mem: [1913, 1913, 1914] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 12.2 % elapsed: 0 min 2 sec remaining: 0
min 11 sec cpu: 112.1 % mem: [1917, 1917, 1917] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 12.2 % elapsed: 0 min 2 sec
remaining: 0 min 11 sec cpu: 112.1 % mem: [1918, 1918, 1918] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 13.3 % elapsed: 0 min 2
sec remaining: 0 min 10 sec cpu: 112.1 % mem: [1918, 1918,
1918] MB [DSK: Pass 1/1, Step 2: counting kmers ] 14.3 % elapsed:
0 min 2 sec remaining: 0 min 9 sec cpu: 112.1 % mem: [1920,
1920, 1920] MB [DSK: Pass 1/1, Step 2: counting kmers ] 15.6 %
elapsed: 0 min 2 sec remaining: 0 min 9 sec cpu: 113.4 %
mem: [1925, 1925, 1925] MB [DSK: Pass 1/1, Step 2: counting kmers ]
16.9 % elapsed: 0 min 2 sec remaining: 0 min 8 sec cpu:
114.0 % mem: [1928, 1928, 1928] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 18.2 % elapsed: 0 min 2 sec remaining: 0 min 7 sec
cpu: 114.0 % mem: [1929, 1929, 1929] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 18.2 % elapsed: 0 min 2 sec remaining: 0
min 7 sec cpu: 114.0 % mem: [1929, 1929, 1930] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 19.2 % elapsed: 0 min 2 sec
remaining: 0 min 7 sec cpu: 114.6 % mem: [1930, 1930, 1931] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 20.5 % elapsed: 0 min 2
sec remaining: 0 min 6 sec cpu: 115.3 % mem: [1932, 1932,
1932] MB [DSK: Pass 1/1, Step 2: counting kmers ] 21.7 % elapsed:
0 min 2 sec remaining: 0 min 6 sec cpu: 115.2 % mem: [1935,
1935, 1935] MB [DSK: Pass 1/1, Step 2: counting kmers ] 22.7 %
elapsed: 0 min 2 sec remaining: 0 min 5 sec cpu: 115.2 %
mem: [1936, 1936, 1936] MB [DSK: Pass 1/1, Step 2: counting kmers ]
23.7 % elapsed: 0 min 2 sec remaining: 0 min 5 sec cpu:
115.2 % mem: [1936, 1936, 1936] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 25 % elapsed: 0 min 2 sec remaining: 0 min 5 sec
cpu: 115.8 % mem: [1940, 1940, 1940] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 26 % elapsed: 0 min 2 sec remaining: 0
min 4 sec cpu: 116.5 % mem: [1940, 1940, 1940] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 26.8 % elapsed: 0 min 2 sec
remaining: 0 min 4 sec cpu: 116.5 % mem: [1940, 1940, 1940] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 28.1 % elapsed: 0 min 2
sec remaining: 0 min 4 sec cpu: 116.5 % mem: [1941, 1941,
1941] MB [DSK: Pass 1/1, Step 2: counting kmers ] 28.1 % elapsed:
0 min 2 sec remaining: 0 min 4 sec cpu: 117.1 % mem: [1942,
1942, 1942] MB [DSK: Pass 1/1, Step 2: counting kmers ] 30.3 %
elapsed: 0 min 2 sec remaining: 0 min 4 sec cpu: 117.1 %
mem: [1942, 1942, 1942] MB [DSK: Pass 1/1, Step 2: counting kmers ]
30.3 % elapsed: 0 min 2 sec remaining: 0 min 4 sec cpu:
117.1 % mem: [1943, 1943, 1943] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 31.3 % elapsed: 0 min 2 sec remaining: 0 min 3 sec
cpu: 117.7 % mem: [1944, 1944, 1944] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 32.4 % elapsed: 0 min 2 sec remaining: 0
min 3 sec cpu: 117.7 % mem: [1944, 1944, 1944] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 33.9 % elapsed: 0 min 2 sec
remaining: 0 min 3 sec cpu: 117.7 % mem: [1945, 1945, 1945] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 34.6 % elapsed: 0 min 2
sec remaining: 0 min 3 sec cpu: 117.7 % mem: [1945, 1945,
1945] MB [DSK: Pass 1/1, Step 2: counting kmers ] 35.8 % elapsed:
0 min 2 sec remaining: 0 min 3 sec cpu: 118.4 % mem: [1946,
1946, 1946] MB [DSK: Pass 1/1, Step 2: counting kmers ] 36.6 %
elapsed: 0 min 2 sec remaining: 0 min 3 sec cpu: 118.4 %
mem: [1946, 1946, 1946] MB [DSK: Pass 1/1, Step 2: counting kmers ]
37.6 % elapsed: 0 min 2 sec remaining: 0 min 3 sec cpu:
118.4 % mem: [1946, 1946, 1946] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 38.8 % elapsed: 0 min 2 sec remaining: 0 min 2 sec
cpu: 118.4 % mem: [1946, 1946, 1946] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 40.2 % elapsed: 0 min 2 sec remaining: 0
min 2 sec cpu: 118.4 % mem: [1946, 1946, 1946] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 40.2 % elapsed: 0 min 2 sec
remaining: 0 min 2 sec cpu: 118.4 % mem: [1946, 1946, 1946] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 41.2 % elapsed: 0 min 2
sec remaining: 0 min 2 sec cpu: 118.4 % mem: [1947, 1947,
1947] MB [DSK: Pass 1/1, Step 2: counting kmers ] 42.5 % elapsed:
0 min 2 sec remaining: 0 min 2 sec cpu: 118.4 % mem: [1947,
1947, 1947] MB [DSK: Pass 1/1, Step 2: counting kmers ] 43.3 %
elapsed: 0 min 2 sec remaining: 0 min 2 sec cpu: 119.0 %
mem: [1949, 1949, 1949] MB [DSK: Pass 1/1, Step 2: counting kmers ]
44.1 % elapsed: 0 min 2 sec remaining: 0 min 2 sec cpu:
119.0 % mem: [1947, 1949, 1949] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 45.6 % elapsed: 0 min 2 sec remaining: 0 min 2 sec
cpu: 119.0 % mem: [1949, 1949, 1949] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 46.7 % elapsed: 0 min 2 sec remaining: 0
min 2 sec cpu: 119.0 % mem: [1949, 1949, 1949] MB [DSK: Pass 1/1,
Step 2: counting kmers ] 47.8 % elapsed: 0 min 2 sec
remaining: 0 min 2 sec cpu: 119.0 % mem: [1949, 1949, 1949] MB
[DSK: Pass 1/1, Step 2: counting kmers ] 48.9 % elapsed: 0 min 2
sec remaining: 0 min 2 sec cpu: 119.0 % mem: [1950, 1950,
1950] MB [DSK: Pass 1/1, Step 2: counting kmers ] 50.2 % elapsed:
0 min 2 sec remaining: 0 min 2 sec cpu: 118.9 % mem: [1950,
1950, 1950] MB [DSK: Pass 1/1, Step 2: counting kmers ] 50.2 %
elapsed: 0 min 2 sec remaining: 0 min 2 sec cpu: 118.9 %
mem: [1950, 1950, 1950] MB [DSK: Pass 1/1, Step 2: counting kmers ]
52.2 % elapsed: 0 min 2 sec remaining: 0 min 1 sec cpu:
118.9 % mem: [1950, 1950, 1950] MB [DSK: Pass 1/1, Step 2: counting
kmers ] 52.2 % elapsed: 0 min 2 sec remaining: 0 min 1 sec
cpu: 118.9 % mem: [1950, 1950, 1950] MB [DSK: Pass 1/1, Step 2:
counting kmers ] 53.4 % elapsed: 0 min 2 sec remaining: 0
min 1 sec cpu: 118.9 % mem: [1950, 1950, 1950] MB [DSK: nb solid
kmers: 1057 ] 53.4 % elapsed: 0 min 2 sec
remaining: 0 min 1 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 2 sec remaining: 0
min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 2 sec
remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 2 sec remaining: 0
min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 2 sec
remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 2 sec remaining: 0
min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 2 sec
remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 2 sec remaining: 0
min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 2 sec
remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers:
1057 ] 100 % elapsed: 0 min 2 sec remaining: 0
min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid
kmers: 1057 ] 100 % elapsed: 0 min 2 sec
remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[DSK: nb solid kmers: 1057 ] 100 % elapsed: 0 min 2
sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952, 1952,
1954] MB [DSK: nb solid kmers: 1057 ] 100 % elapsed:
0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 % mem: [1952,
1952, 1954] MB [DSK: nb solid kmers: 1057 ] 100 %
elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu: 118.3 %
mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057 ]
100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec cpu:
118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0 sec
cpu: 118.3 % mem: [1952, 1952, 1954] MB [DSK: nb solid kmers: 1057
] 100 % elapsed: 0 min 2 sec remaining: 0 min 0
sec cpu: 118.3 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 0 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 1.89 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 2.84 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [1952, 1952, 1954] MB [Bloom: read solid kmers ]
3.78 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 4.73 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 5.68 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 6.62 % elapsed: 0 min 0 sec remaining: 0 min
0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid
kmers ] 7.57 % elapsed: 0 min 0 sec remaining:
0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read
solid kmers ] 8.51 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 9.46 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 10.4 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 11.4 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [1952, 1952, 1954] MB [Bloom: read solid kmers ]
12.3 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 13.2 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 14.2 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 15.1 % elapsed: 0 min 0 sec remaining: 0 min
0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid
kmers ] 16.1 % elapsed: 0 min 0 sec remaining:
0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read
solid kmers ] 17 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 18.9 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 19.9 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 20.8 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [1952, 1952, 1954] MB [Bloom: read solid kmers ]
21.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
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] 22.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 23.7 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 24.6 % elapsed: 0 min 0 sec remaining: 0 min
0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid
kmers ] 25.5 % elapsed: 0 min 0 sec remaining:
0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read
solid kmers ] 26.5 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 27.4 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 28.4 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 29.3 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [1952, 1952, 1954] MB [Bloom: read solid kmers ]
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-1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 31.2 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 32.2 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 33.1 % elapsed: 0 min 0 sec remaining: 0 min
0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid
kmers ] 34.1 % elapsed: 0 min 0 sec remaining:
0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read
solid kmers ] 35 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 36.9 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 37.8 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 38.8 %
elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 %
mem: [1952, 1952, 1954] MB [Bloom: read solid kmers ]
39.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu:
-1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 40.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec
cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 41.6 % elapsed: 0 min 0 sec remaining: 0 min 0
sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid kmers
] 42.6 % elapsed: 0 min 0 sec remaining: 0 min
0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read solid
kmers ] 43.5 % elapsed: 0 min 0 sec remaining:
0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB [Bloom: read
solid kmers ] 44.5 % elapsed: 0 min 0 sec
remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952, 1954] MB
[Bloom: read solid kmers ] 45.4 % elapsed: 0 min 0
sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952, 1952,
1954] MB [Bloom: read solid kmers ] 46.4 % elapsed:
0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [1952,
1952, 1954] MB [Bloom: read solid kmers ] 47.3 %
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cpu: 200.0 % mem: [1952, 1953, 1954] MB graph
gatb-core-library version
: 1.4.2
git_sha1 : notset
build_date : 2021-10-18/11:51:05
build_system : Linux-5.10.0-9-amd64
build_compiler : /usr/bin/cc (11.2.0)
build_kmer_size : 32 64 96 128
host name
: ci-303-f6feacb6
nb_cores : 48
memory : 251.8
disk_current_dir : 2076.3
max_file_nb : 1024
pid : 1942
configuration config
kmer_size
: 31
mini_size : 10
solidity_kind : one
abundance_min : 3
abundance_max : 2147483647
available_space : 2126129
estimated_sequence_number : 620
estimated_sequence_volume : 0
estimated_kmers_number : 43400
estimated_kmers_volume : 1
max_disk_space : 2124129
max_memory : 5000
nb_passes : 1
nb_partitions : 48
nb_bits_per_kmer : 64
nb_cores : 48
minimizer_type : lexicographic
(kmc2 heuristic)
repartition_type : unordered
nb_cores_per_partition : 1
nb_partitions_in_parallel : 48
nb_cached_items_per_core_per_part : 32768
nb_banks : 2
system cpu
: -1.0
repartition system
cpu
: 92.3
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 : 48
nb_items : 1057
part_biggest : 38
part_smallest : 11
part_mean : 22.0
kind
vector : 48
fillsolid_time : 0.003
1.read : 0.002
2.sort : 0.001
3.dump : 0.000
time : 1.649
fill_partitions : 1.551
fill_solid_kmers : 0.098
system cpu
: 118.1
bloom stats
kind
: neighbor
bitsize : 6378
nb_hash : 4
nbits_per_kmer : 6.034370
time : 0.006
build_from_kmers : 0.006
system cpu
: 100.0
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 : 0.175
cascading : 0.017
fill_debloom_file : 0.142
finalize_debloom_file : 0.016
system cpu
: 177.3
branching stats
nb_branching : 8
percentage : 0.8
checksum_branching : c26285a84228c6e7
time build
: 0.009
system cpu
: 200.0
Graph creation time in seconds: 2
rm -rf trashme_1942_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 550: 5066 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 [11:09:25]: test run-unit-test
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