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 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-1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 89.9 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 90.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 91.8 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 92.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 93.7 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 94.6 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 95.6 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 96.5 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 97.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 98.4 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: build branching nodes ] 99.3 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB [Graph: nb branching found : 8 ] 99.3 % elapsed: 0 min 0 sec remaining: 0 min 0 sec cpu: -1.0 % mem: [ 37, 37, 847] MB graph 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
