[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_amd64_12 #29166
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sat Mar 12 16:35:36 UTC 2016
See <https://jenkins.debian.net/job/reproducible_builder_amd64_12/29166/>
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make[4]: Leaving directory '/build/spades-3.7.0+dfsg/build_spades'
[ 99%] Built target corrector
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Scanning dependencies of target scaffold_correction
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[100%] Building CXX object scaffold_correction/CMakeFiles/scaffold_correction.dir/main.cpp.o
[100%] Linking CXX executable ../bin/scaffold_correction
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[100%] Built target scaffold_correction
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[ 14%] Built target nlopt
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[ 28%] Built target yaml-cpp
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[ 35%] Built target ConsensusCore
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[ 55%] Built target BamTools
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[ 63%] Built target samtools
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[ 64%] Built target format
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[ 66%] Built target ssw
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[ 67%] Built target cityhash
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[ 71%] Built target input
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[ 84%] Built target debruijn
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[ 85%] Built target spades
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[ 89%] Built target hammer
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[ 94%] Built target ionhammer
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[ 96%] Built target dipspades
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[ 99%] Built target corrector
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[100%] Built target scaffold_correction
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Install the project...
-- Install configuration: "RelWithAsserts"
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/spades.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/truspades.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/dipspades.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/spades_init.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/VERSION
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/genes_1K.gff
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/operons_1K.txt
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/genes_1K.txt
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/reference_1K.fa.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/operons_1K.gff
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset_truspades
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset_truspades/B_R2.fastq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset_truspades/A_R2.fastq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset_truspades/B_R1.fastq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset_truspades/A_R1.fastq.gz
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/manual.html
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/dipspades_manual.html
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/truspades_manual.html
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/LICENSE
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/GPLv2.txt
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/spades
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/simplification.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/config.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/path_extend
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/path_extend/pe_params.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/tsa.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/distance_estimation.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/construction.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/debruijn/detail_info_printer.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/hammer
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/hammer
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/hammer/config.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/ionhammer
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/ionhammer
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/ionhammer/ionhammer.cfg.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/hammer_logic.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/process_cfg.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/spades_logic.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/dipspades_logic.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/corrector_logic.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/support.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/options_storage.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/lucigen_nxmate.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/reference_construction.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_filter_contigs.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/break_by_coverage.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/moleculo_postprocessing.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/barcode_extraction.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/generate_quality.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/id_generation.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/launch_options.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/truspades/string_dist_utils.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/common/alignment.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/common/parallel_launcher.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/common/sam_parser.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/spades_pipeline/common/SeqIO.py
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/dipspades
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/dipspades
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/dipspades/config.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/corrector
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/corrector
-- Installing: /build/spades-3.7.0+dfsg/install_spades/share/spades/configs/corrector/corrector.info.template
-- Installing: /build/spades-3.7.0+dfsg/install_spades/bin/scaffold_correction
make[2]: Leaving directory '/build/spades-3.7.0+dfsg/build_spades'
make[1]: Leaving directory '/build/spades-3.7.0+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/spades-3.7.0+dfsg'
/build/spades-3.7.0+dfsg/install_spades/bin/spades.py --test
== Warning == Spades is using local bwa at /usr/bin/bwa.
Command line: /build/spades-3.7.0+dfsg/install_spades/bin/spades.py --test
System information:
SPAdes version: 3.7.0
Python version: 2.7.11
OS: Linux-3.16.0-4-amd64-x86_64-with-debian-stretch-sid
Output dir: /build/spades-3.7.0+dfsg/spades_test
Mode: read error correction and assembling
Debug mode is turned OFF
Dataset parameters:
Multi-cell mode (you should set '--sc' flag if input data was obtained with MDA (single-cell) technology or --meta flag if processing metagenomic dataset)
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads: ['/build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz']
right reads: ['/build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz']
interlaced reads: not specified
single reads: not specified
Read error correction parameters:
Iterations: 1
PHRED offset will be auto-detected
Corrected reads will be compressed (with gzip)
Assembly parameters:
k: automatic selection based on read length
Mismatch careful mode is turned OFF
Repeat resolution is enabled
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Other parameters:
Dir for temp files: /build/spades-3.7.0+dfsg/spades_test/tmp
Threads: 16
Memory limit (in Gb): 47
======= SPAdes pipeline started. Log can be found here: /build/spades-3.7.0+dfsg/spades_test/spades.log
===== Read error correction started.
== Running read error correction tool: /build/spades-3.7.0+dfsg/install_spades/bin/hammer /build/spades-3.7.0+dfsg/spades_test/corrected/configs/config.info
0:00:00.000 20M / 42M INFO General (main.cpp : 85) Starting BayesHammer, built from N/A, git revision N/A
0:00:00.000 20M / 42M INFO General (main.cpp : 86) Loading config from /build/spades-3.7.0+dfsg/spades_test/corrected/configs/config.info
0:00:00.002 20M / 42M INFO General (memory_limit.hpp : 44) Memory limit set to 47 Gb
0:00:00.002 20M / 42M INFO General (main.cpp : 95) Trying to determine PHRED offset
0:00:00.002 20M / 42M INFO General (main.cpp : 101) Determined value is 33
0:00:00.002 20M / 42M INFO General (hammer_tools.cpp : 36) Hamming graph threshold tau=1, k=21, subkmer positions = [ 0 10 ]
0:00:00.002 20M / 42M INFO General (main.cpp : 122) Size of aux. kmer data 24 bytes
=== ITERATION 0 begins ===
0:00:00.002 20M / 42M INFO K-mer Index Building (kmer_index.hpp : 470) Building kmer index
0:00:00.002 20M / 42M INFO K-mer Splitting (kmer_data.cpp : 142) Splitting kmer instances into 256 buckets. This might take a while.
0:00:00.003 20M / 42M INFO General (file_limit.hpp : 30) Open file limit set to 65536
0:00:00.003 20M / 42M INFO K-mer Splitting (kmer_data.cpp : 160) Memory available for splitting buffers: 0.97876 Gb
0:00:00.003 20M / 42M INFO K-mer Splitting (kmer_data.cpp : 168) Using cell size of 262144
0:00:00.145 8G / 53M INFO K-mer Splitting (kmer_data.cpp : 182) Processing /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz
0:00:00.497 8G / 71M INFO K-mer Splitting (kmer_data.cpp : 182) Processing /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz
0:00:00.591 8G / 71M INFO K-mer Splitting (kmer_data.cpp : 196) Processed 4108 reads
0:00:00.705 37G / 71M INFO General (kmer_index.hpp : 348) Starting k-mer counting.
0:00:00.992 37G / 71M INFO General (kmer_index.hpp : 354) K-mer counting done. There are 1974 kmers in total.
0:00:00.992 37G / 71M INFO General (kmer_index.hpp : 356) Merging temporary buckets.
0:00:01.021 37G / 71M INFO K-mer Index Building (kmer_index.hpp : 479) Building perfect hash indices
0:00:01.052 37G / 71M INFO General (kmer_index.hpp : 374) Merging final buckets.
0:00:01.057 37G / 71M INFO K-mer Index Building (kmer_index.hpp : 527) Index built. Total 792 bytes occupied (3.20973 bits per kmer).
0:00:01.058 37G / 71M INFO K-mer Counting (kmer_data.cpp : 519) Arranging kmers in hash map order
0:00:01.069 37G / 71M INFO General (main.cpp : 157) Clustering Hamming graph.
0:00:01.097 37G / 71M INFO General (main.cpp : 164) Extracting clusters
0:00:01.118 37G / 71M INFO General (main.cpp : 176) Clustering done. Total clusters: 1960
0:00:01.118 37G / 71M INFO K-mer Counting (kmer_data.cpp : 541) Collecting K-mer information, this takes a while.
0:00:01.118 37G / 71M INFO K-mer Counting (kmer_data.cpp : 547) Processing /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz
0:00:01.169 37G / 71M INFO K-mer Counting (kmer_data.cpp : 547) Processing /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz
0:00:01.221 37G / 71M INFO K-mer Counting (kmer_data.cpp : 554) Collection done, postprocessing.
0:00:01.221 37G / 71M INFO K-mer Counting (kmer_data.cpp : 568) There are 1974 kmers in total. Among them 0 (0%) are singletons.
0:00:01.221 37G / 71M INFO General (main.cpp : 182) Subclustering Hamming graph
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 647) Subclustering done. Total 0 non-read kmers were generated.
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 648) Subclustering statistics:
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 649) Total singleton hamming clusters: 1946. Among them 1946 (100%) are good
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 650) Total singleton subclusters: 8. Among them 8 (100%) are good
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 651) Total non-singleton subcluster centers: 10. Among them 10 (100%) are good
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 652) Average size of non-trivial subcluster: 2.8 kmers
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 653) Average number of sub-clusters per non-singleton cluster: 1.28571
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 654) Total solid k-mers: 1964
0:00:01.241 37G / 71M INFO Hamming Subclustering (kmer_cluster.cpp : 655) Substitution probabilities: [4,4]((0.875,0.125,0,0),(0,1,0,0),(0,0,1,0),(0,0,0.125,0.875))
0:00:01.242 37G / 71M INFO General (main.cpp : 187) Finished clustering.
0:00:01.242 37G / 71M INFO General (main.cpp : 206) Starting solid k-mers expansion in 16 threads.
0:00:01.287 37G / 71M INFO General (main.cpp : 227) Solid k-mers iteration 0 produced 0 new k-mers.
0:00:01.287 37G / 71M INFO General (main.cpp : 231) Solid k-mers finalized
0:00:01.287 37G / 71M INFO General (hammer_tools.cpp : 210) Starting read correction in 16 threads.
0:00:01.287 37G / 71M INFO General (hammer_tools.cpp : 221) Correcting pair of reads: /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_1.fq.gz and /build/spades-3.7.0+dfsg/install_spades/share/spades/test_dataset/ecoli_1K_2.fq.gz
Terminated
Sat 12 Mar 16:35:35 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-SSygzsgm, which will now be removed.
/srv/reproducible-results/rbuild-debian-s2bpdSAA/tmp.q0huAPxJhz: 40.2% -- replaced with /srv/reproducible-results/rbuild-debian-s2bpdSAA/tmp.q0huAPxJhz.gz
Sat 12 Mar 16:35:35 UTC 2016 - /srv/jenkins/bin/reproducible_build.sh stopped running as /tmp/jenkins-script-SSygzsgm, which will now be removed.
INFO: Starting at 2016-03-12 16:35:36.069940
INFO: Finished at 2016-03-12 16:35:36.098651, took: 0:00:00.028725
FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1738)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:410)
INFO: Starting at 2016-03-12 16:35:36.605278
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