Your message dated Wed, 07 Aug 2024 16:49:44 +0000 with message-id <e1sbjr6-00ck8k...@fasolo.debian.org> and subject line Bug#1074658: fixed in kissplice 2.6.7-1 has caused the Debian Bug report #1074658, regarding kissplice: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit code 2 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.) -- 1074658: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1074658 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: kissplice Version: 2.6.2-3 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20240702 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > Running tests... > /usr/bin/ctest --force-new-ctest-process --verbose -j8 > UpdateCTestConfiguration from > :/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/DartConfiguration.tcl > UpdateCTestConfiguration from > :/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/DartConfiguration.tcl > Test project /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu > Constructing a list of tests > Done constructing a list of tests > Updating test list for fixtures > Added 0 tests to meet fixture requirements > Checking test dependency graph... > Checking test dependency graph end > test 1 > Start 1: IsBcalmStartable > > 1: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice/bcalm > "-help" > 1: Working Directory: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests > 1: Test timeout computed to be: 10000000 > test 2 > Start 2: KisspliceBasicTest > > 2: Test command: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice "-h" > 2: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/integration_tests > 2: Test timeout computed to be: 10000000 > test 3 > Start 3: KisspliceDBGTest > > 3: Test command: /<<PKGBUILDDIR>>/tests/integration_tests/kisspliceDBGTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin" > 3: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/integration_tests > 3: Test timeout computed to be: 10000000 > test 4 > Start 4: KisspliceTwoSequencesTest > > 4: Test command: > /<<PKGBUILDDIR>>/tests/integration_tests/kisspliceTwoSequencesTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin" > 4: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/integration_tests > 4: Test timeout computed to be: 10000000 > test 5 > Start 5: KisspliceGraphAndSequenceTest > > 5: Test command: > /<<PKGBUILDDIR>>/tests/integration_tests/kisspliceGraphAndSequenceTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin" > 5: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/integration_tests > 5: Test timeout computed to be: 10000000 > test 6 > Start 6: KisspliceGraphTest > > 6: Test command: > /<<PKGBUILDDIR>>/tests/integration_tests/kisspliceGraphTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin" > 6: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/integration_tests > 6: Test timeout computed to be: 10000000 > test 7 > Start 7: ksBubbleEnumerationTest > > 7: Test command: > /<<PKGBUILDDIR>>/tests/functional_tests/ksBubbleEnumerationTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice" > 7: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/functional_tests > 7: Test timeout computed to be: 10000000 > test 8 > Start 8: ksRunModulesTest > > 8: Test command: /<<PKGBUILDDIR>>/tests/functional_tests/ksRunModulesTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice" > 8: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/functional_tests > 8: Test timeout computed to be: 10000000 > 1: > 1: [bcalm_1 options] > 1: -nb-cores (1 arg) : number of cores [default '0'] > 1: -verbose (1 arg) : verbosity level [default '1'] > 1: -version (0 arg) : version > 1: -help (0 arg) : help > 1: > 1: [graph options] > 1: -no-mphf (0 arg) : don't construct the MPHF > 1: > 1: [kmer count options] > 1: -in (1 arg) : reads > file [default ''] > 1: -kmer-size (1 arg) : size of > a kmer [default '31'] > 1: -abundance-min (1 arg) : min > abundance threshold for solid kmers [default '2'] > 1: -abundance-max (1 arg) : max > abundance threshold for solid kmers [default '2147483647'] > 1: -solidity-custom (1 arg) : when > solidity-kind is custom, specifies list of files where kmer must be present > [default ''] > 1: -max-memory (1 arg) : max > memory (in MBytes) [default '5000'] > 1: -max-disk (1 arg) : max disk > (in MBytes) [default '0'] > 1: -out (1 arg) : output > file [default ''] > 1: -out-dir (1 arg) : output > directory [default '.'] > 1: -out-tmp (1 arg) : output > directory for temporary files [default '.'] > 1: -out-compress (1 arg) : h5 > compression level (0:none, 9:best) [default '0'] > 1: -storage-type (1 arg) : storage > type of kmer counts ('hdf5' or 'file') [default 'hdf5'] > 1: -histo2D (1 arg) : compute > the 2D histogram (with first file = genome, remaining files = reads) > [default '0'] > 1: -histo (1 arg) : output > the kmer abundance histogram [default '0'] > 1: > 1: [kmer count, advanced performance tweaks options] > 1: -minimizer-type (1 arg) : minimizer type (0=lexi, > 1=freq) [default '1'] > 1: -minimizer-size (1 arg) : size of a minimizer > [default '10'] > 1: -repartition-type (1 arg) : minimizer repartition > (0=unordered, 1=ordered) [default '1'] > 1: > 1: [bloom options] > 1: -bloom (1 arg) : bloom type ('basic', 'cache', > 'neighbor') [default 'neighbor'] > 1: -debloom (1 arg) : debloom type ('none', 'original' > or 'cascading') [default 'cascading'] > 1: -debloom-impl (1 arg) : debloom impl ('basic', > 'minimizer') [default 'minimizer'] > 1: > 1: [branching options] > 1: -branching-nodes (1 arg) : branching type ('none' or > 'stored') [default 'stored'] > 1: -topology-stats (1 arg) : topological information level > (0 for none) [default '0'] > 1: > 1: [general options] > 1: -config-only (0 arg) : dump config only > 1: -nb-cores (1 arg) : number of cores [default > '0'] > 1: -all-abundance-counts (0 arg) : output all k-mer abundance > counts instead of mean > 1: -edge-km (1 arg) : edge km representation > [default '0'] > 1: -verbose (1 arg) : verbosity level [default > '1'] > 1: -integer-precision (1 arg) : integers precision (0 for > optimized value) [default '0'] > 1: > 1: [debug options] > 1: -redo-bcalm (0 arg) : debug function, redo the > bcalm algo > 1: -skip-bcalm (0 arg) : same, but skip > bcalm > 1: -redo-bglue (0 arg) : same, but redo > bglue (needs debug_keep_glue_files=true in source code) > 1: -skip-bglue (0 arg) : same, but skip > bglue > 1: -redo-links (0 arg) : same, but redo > links > 1: -skip-links (0 arg) : same, but skip > links > 1: -nb-glue-partitions (1 arg) : number of glue partitions > (automatically calculated by default) [default '0'] > 1/9 Test #1: IsBcalmStartable ................. Passed 0.02 sec > test 9 > Start 9: ksErrorRemovalTest > > 9: Test command: > /<<PKGBUILDDIR>>/tests/functional_tests/ksErrorRemovalTest.py > "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice" > 9: Working Directory: > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/tests/functional_tests > 9: Test timeout computed to be: 10000000 > 2: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\d' > 2: retype = re.compile('Type_\d+') > 2: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: SyntaxWarning: > invalid escape sequence '\d' > 2: retype = re.compile('Type_\d+') > 2: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: SyntaxWarning: > invalid escape sequence '\d' > 2: retype = re.compile('Type_\d+') > 7: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice/ks_bubble_enumeration > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_info_bcc > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_contents_edges_bcc > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_contents_nodes_bcc > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_all_edges_bcc > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_all_nodes_bcc 2 25 > /<<PKGBUILDDIR>>/tests/functional_tests/data/test_ks_bubble_enumeration_output > 3 bcc_test 0 -u 1000 -L 49 -l 42 -M 10000 -b 5 > 7: b'\t Enumerating bubbles with at most 5 branching nodes in each > path!\n============================================================================\nSummary > of > results\n============================================================================\nNo > of bubbles: > 4\n============================================================================\n' > 7: Ks_Bubble_Enumeration_Test: test SUCCESSFUL > 2/9 Test #7: ksBubbleEnumerationTest .......... Passed 0.06 sec > 9: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice/ks_error_removal > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges > > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance > 0.02/<<PKGBUILDDIR>>/tests/functional_tests/data/test_ks_error_removal_output > 9: b'252 out of 5336 edges removed\n' > 9: ks_error_removal: test SUCCESSFUL > 8: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/lib/kissplice/ks_run_modules > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges > > /<<PKGBUILDDIR>>/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes > 25 > /<<PKGBUILDDIR>>/tests/functional_tests/data/test_ks_run_modules_output_graph > 8: b'Searching biconnected components...\nNumber of biconnected components > found: 109\n\nProcessing component 1...\nInitial size: 4 nodes.\nCompressing > linear paths...\nNumber of compressed nodes: 0.\nCompressing simple > bubbles...\nNumber of compressed bubbles: 0.\nRecompressing linear > paths...\nNumber of compressed nodes: 0.\nFinal size: 4 > nodes.\nDone!\n\nProcessing component 2...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 3...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 4...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 5...\nInitial size: 9 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 8 nodes.\nDone!\n\nProcessing component 6...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 7...\nInitial size: 41 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 11.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 30 nodes.\nDone!\n\nProcessing component 8...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 9...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 10...\nInitial size: 68 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 4.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 64 nodes.\nDone!\n\nProcessing component 11...\nInitial size: 54 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 5.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 49 nodes.\nDone!\n\nProcessing component 12...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 13...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 14...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 15...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 16...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 17...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 18...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 19...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 20...\nInitial size: 37 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 37 nodes.\nDone!\n\nProcessing component 21...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 22...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 23...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 24...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 25...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 26...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 27...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 28...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 29...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 30...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 31...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 32...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 33...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 34...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 35...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 6 nodes.\nDone!\n\nProcessing component 36...\nInitial size: 9 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 8 nodes.\nDone!\n\nProcessing component 37...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 38...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 39...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 40...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 41...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 42...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 43...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 44...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 45...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 46...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 47...\nInitial size: 13 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 8.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 48...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 49...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 50...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 51...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 52...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 53...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 54...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 55...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 56...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 57...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 58...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 59...\nInitial size: 8 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 6 nodes.\nDone!\n\nProcessing component 60...\nInitial size: 9 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 8 nodes.\nDone!\n\nProcessing component 61...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 62...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 63...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 64...\nInitial size: 8 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 7 nodes.\nDone!\n\nProcessing component 65...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 66...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 67...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 68...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 69...\nInitial size: 3 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 1 nodes.\nDone!\n\nProcessing component 70...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 4.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 1 nodes.\nDone!\n\nProcessing component 71...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 72...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 73...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 74...\nInitial size: 29 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 8.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 21 nodes.\nDone!\n\nProcessing component 75...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 2.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 76...\nInitial size: 8 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 3.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 3.\nFinal > size: 1 nodes.\nDone!\n\nProcessing component 77...\nInitial size: 6 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 6 nodes.\nDone!\n\nProcessing component 78...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 79...\nInitial size: 7 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 3.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 80...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 81...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 82...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 83...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 84...\nInitial size: 8 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 8 nodes.\nDone!\n\nProcessing component 85...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 86...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 87...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 88...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 89...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 90...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 91...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 92...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 93...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 94...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 1.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 95...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 96...\nInitial size: 33 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 5.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 28 nodes.\nDone!\n\nProcessing component 97...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 98...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 99...\nInitial size: 5 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 5 nodes.\nDone!\n\nProcessing component 100...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 101...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 102...\nInitial size: 14 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 14 nodes.\nDone!\n\nProcessing component 103...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 104...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 105...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 0.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 4 nodes.\nDone!\n\nProcessing component 106...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 107...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 108...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\nProcessing component 109...\nInitial size: 4 > nodes.\nCompressing linear paths...\nNumber of compressed nodes: > 0.\nCompressing simple bubbles...\nNumber of compressed bubbles: > 1.\nRecompressing linear paths...\nNumber of compressed nodes: 0.\nFinal > size: 3 nodes.\nDone!\n\n' > 8: ks_run_modules: test SUCCESSFUL > 3/9 Test #9: ksErrorRemovalTest ............... Passed 0.08 sec > 4/9 Test #8: ksRunModulesTest ................. Passed 0.10 sec > 2: usage: kissplice [-h] [-r READFILES] [-k KVAL] [-b BVAL] [-l LLMAX] > 2: [-m LL_MIN] [-M UL_MAX] [-g GRAPH_PREFIX] [-o OUT_DIR] > 2: [-d PATH_TO_TMP] [-t NBPROCS] [-s OUTPUT_SNPS] [-v] [-u] > 2: [-c MIN_COV] [-C MIN_RELATIVE_COV] [-e MIN_EDIT_DIST] > 2: [-y MAX_CYCLES] [--mismatches MISM] [--mismatchesSNP > MISMSNP] > 2: [--counts COUNTSMETHOD] [--min_overlap MINOVERLAP] > 2: [--timeout TIMEOUT] [--version] [--output-context] > 2: [--output-path] [--output-branch-count] [--keep-bccs] > 2: [--not-experimental] [--max-memory MAX_MEMORY] > 2: [--keep-counts] [--get-mapping-info] [--stranded] > 2: [--strandedAbsoluteThreshold STRANDEDABSOLUTETHRESHOLD] > 2: [--strandedRelativeThreshold STRANDEDRELATIVETHRESHOLD] > 2: [--keep-redundancy] [--keep-low-complexity] > 2: [--lc-entropy-threshold LC_ENT] [--get-redundance-info] > 2: [--get-low-complexity-info] [--type1-only] > 2: > 2: kisSplice - local assembly of SNPs, indels and AS events > 2: > 2: options: > 2: -h, --help show this help message and exit > 2: -r READFILES input fasta/q read files or compressed (.gz) > fasta/q > 2: files (mutiple, such as "-r file1 -r file2...") > 2: -k KVAL k-mer size (default=41) > 2: -b BVAL maximum number of branching nodes (default 5) > 2: -l LLMAX maximal length of the shorter path (default: 2k+1) > 2: -m LL_MIN minimum length of the shorter path (default 2k-8) > 2: -M UL_MAX maximum length of the longest path (default > 1000000), > 2: skipped exons longer than UL_MAX are not reported > 2: -g GRAPH_PREFIX path and prefix to pre-built de Bruijn graph > (suffixed > 2: by .edges/.nodes) if jointly used with -r, graph > used > 2: to find bubbles and reads used for quantification > 2: -o OUT_DIR path to store the results and the summary log file > 2: (default = ./results) > 2: -d PATH_TO_TMP specific directory (absolute path) where to build > 2: temporary files (default temporary directory > 2: otherwise) > 2: -t NBPROCS number of cores (must be <= number of physical > cores) > 2: -s OUTPUT_SNPS 0, 1 or 2. Changes which types of SNPs will be > output. > 2: If 0 (default), will not output SNPs. If 1, will > 2: output Type0a-SNPs. If 2, will output Type0a and > 2: Type0b SNPs (warning: this option may increase a > lot > 2: the running time. You might also want to try the > 2: experimental algorithm here) > 2: -v Verbose mode > 2: -u keep the nodes/edges file for unfinished bccs > 2: -c MIN_COV an integer, k-mers present strictly less than this > 2: number of times in the dataset will be discarded > 2: (default 2) > 2: -C MIN_RELATIVE_COV a percentage from [0,1), edges with relative > coverage > 2: below this number are removed (default 0.05) > 2: -e MIN_EDIT_DIST edit distance threshold, if the two sequences > (paths) > 2: of a bubble have edit distance smaller than this > 2: threshold, the bubble is classified as an inexact > 2: repeat (default 3) > 2: -y MAX_CYCLES maximal number of bubbles enumeration in each bcc. > If > 2: exceeded, no bubble is output for the bcc (default > 2: 100M) > 2: --mismatches MISM Maximal number of substitutions authorized between > a > 2: read and a fragment (for quantification only), > default > 2: 2. If you increase the mismatch and use --counts > think > 2: of increasing min_overlap too. > 2: --mismatchesSNP MISMSNP > 2: Maximal number of substitutions authorized between > a > 2: read and a fragment (for quantification only) for > SNP, > 2: default 0. > 2: --counts COUNTSMETHOD > 2: 0,1 or 2 . Changes how the counts will be > reported. If > 2: 0 : total counts, if 1: counts on junctions, if 2 > 2: (default): all counts. see User guide for more > 2: information > 2: --min_overlap MINOVERLAP > 2: Set how many nt must overlap a junction to be > counted > 2: by --counts option. Default=5. see User guide for > more > 2: information > 2: --timeout TIMEOUT max amount of time (in seconds) spent for > enumerating > 2: bubbles in each bcc. If exceeded, no bubble is > output > 2: for the bcc (default 100000) > 2: --version show program's version number and exit > 2: --output-context Will output the maximum non-ambiguous context of a > 2: bubble > 2: --output-path Will output the id of the nodes composing the two > 2: paths of the bubbles. > 2: --output-branch-count > 2: Will output the number of branching nodes in each > 2: path. > 2: --keep-bccs Keep the node/edges files for all bccs. > 2: --not-experimental Do not use a new experimental algorithm that > searches > 2: for bubbles by listing all paths. > 2: --max-memory MAX_MEMORY > 2: If you use the experimental algorithm, you must > 2: provide the maximum size of the process's virtual > 2: memory (address space) in megabytes (default > 2: unlimited). WARNING: this option does not work on > Mac > 2: operating systems. > 2: --keep-counts Keep the .counts file after the sequencing-errors- > 2: removal step. > 2: --get-mapping-info Creates a file with the KissReads mapping > information > 2: of the reads on the bubbles. > 2: --stranded Execute kissreads in stranded mode. > 2: --strandedAbsoluteThreshold STRANDEDABSOLUTETHRESHOLD > 2: Sets the minimum number of reads mapping to a path > of > 2: a bubble in a read set is needed to call a strand. > 2: --strandedRelativeThreshold STRANDEDRELATIVETHRESHOLD > 2: If a strand is called for a path of a bubble in a > read > 2: set, but the proportion of reads calling this > strand > 2: is less than this threshold, then the strand of the > 2: path is set to '?' (any strand - not enough > evidence > 2: to call a strand). > 2: --keep-redundancy Keep the Type_1 redundant cycles in the result > file. > 2: --keep-low-complexity > 2: Keep the low-complexity Type_1 cycles in the result > 2: file. > 2: --lc-entropy-threshold LC_ENT > 2: Cycles with a Shannon entropy value for their upper > 2: path below this value will be removed (use > --keep-low- > 2: complexity to keep them). > 2: --get-redundance-info > 2: Creates files with informations on compressed > 2: redundant cycles. > 2: --get-low-complexity-info > 2: Creates a file with informations on removed low- > 2: complexity cycles. > 2: --type1-only Only quantify Type 1 bubbles (alternative splicing > 2: events, MAJOR SPEED UP with -b > 10 BUT all other > 2: bubbles will not appear in the result file). > 5/9 Test #2: KisspliceBasicTest ............... Passed 0.14 sec > 6: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g > /<<PKGBUILDDIR>>/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -C 0 > 6: Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > 6/9 Test #6: KisspliceGraphTest ...............***Failed Required regular > expression not found. Regex=[test SUCCESSFUL > ] 0.55 sec > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g > /<<PKGBUILDDIR>>/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -C 0 > Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > > 5: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g > /<<PKGBUILDDIR>>/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -r /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75brain_100000.fasta -C 0 > 5: Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > 7/9 Test #5: KisspliceGraphAndSequenceTest ....***Failed Required regular > expression not found. Regex=[test SUCCESSFUL > ] 1.02 sec > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -g > /<<PKGBUILDDIR>>/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -r /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75brain_100000.fasta -C 0 > Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > > 3: Traceback (most recent call last): > 3: File "/<<PKGBUILDDIR>>/tests/integration_tests/kisspliceDBGTest.py", > line 16, in <module> > 3: assert result.stderr == b"" > 3: ^^^^^^^^^^^^^^^^^^^^ > 3: AssertionError > 8/9 Test #3: KisspliceDBGTest .................***Failed 4.54 sec > Traceback (most recent call last): > File "/<<PKGBUILDDIR>>/tests/integration_tests/kisspliceDBGTest.py", line > 16, in <module> > assert result.stderr == b"" > ^^^^^^^^^^^^^^^^^^^^ > AssertionError > > 4: /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r > /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75brain_100000.fasta -r > /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75liver_100000.fasta -C 0 > 4: Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > 9/9 Test #4: KisspliceTwoSequencesTest ........***Failed Required regular > expression not found. Regex=[test SUCCESSFUL > ] 4.88 sec > /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice -s 2 -k 25 -M 1000 -r > /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75brain_100000.fasta -r > /<<PKGBUILDDIR>>/tests/integration_tests/data/HBM75liver_100000.fasta -C 0 > Integration test error : > b"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:553: SyntaxWarning: > invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1209: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/bin/kissplice:1253: > SyntaxWarning: invalid escape sequence '\\d'\n retype = > re.compile('Type_\\d+')\n" > > > 56% tests passed, 4 tests failed out of 9 > > Total Test time (real) = 4.89 sec > > The following tests FAILED: > 3 - KisspliceDBGTest (Failed) > 4 - KisspliceTwoSequencesTest (Failed) > 5 - KisspliceGraphAndSequenceTest (Failed) > 6 - KisspliceGraphTest (Failed) > Errors while running CTest > make[1]: *** [Makefile:74: test] Error 8 > make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test > ARGS\+=--verbose ARGS\+=-j8 returned exit code 2 The full build log is available from: http://qa-logs.debian.net/2024/07/02/kissplice_2.6.2-3_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240702;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240702&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
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--- Begin Message ---Source: kissplice Source-Version: 2.6.7-1 Done: Pierre Gruet <p...@debian.org> We believe that the bug you reported is fixed in the latest version of kissplice, 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 1074...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Pierre Gruet <p...@debian.org> (supplier of updated kissplice 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: SHA512 Format: 1.8 Date: Wed, 07 Aug 2024 17:30:12 +0200 Source: kissplice Architecture: source Version: 2.6.7-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Pierre Gruet <p...@debian.org> Closes: 1073482 1074658 Changes: kissplice (2.6.7-1) unstable; urgency=medium . $ Team upload * Advertising repacking with +dfsg suffix for upcoming upstream versions * Shipping the Python file directly in /usr/bin, not symlinking to /usr/share/kissplice anymore * Adding internal binaries in a subdir of /usr/lib/${DEB_HOST_MULTIARCH} . [ François Gindraud ] * Propagate upstream build system changes for bcalm and guide * Fix dh_auto_clean . [ Andreas Tille ] * New upstream version Closes: #1073482, #1074658 * Standards-Version: 4.7.0 (routine-update) Checksums-Sha1: e0a46e669b02703101443ef58d0bbc4bab617c8e 2307 kissplice_2.6.7-1.dsc 31c34f0a4a0c0432ff4d257b30b93dadd6121db1 4583195 kissplice_2.6.7.orig.tar.bz2 a2a89807a18c6f85f0dbcbd3ed24fcf92ba6c09a 6740 kissplice_2.6.7-1.debian.tar.xz 521a770659fde617dee34ef71ba886c1acac0b85 8966 kissplice_2.6.7-1_source.buildinfo Checksums-Sha256: c853663a23685b50e7d5dcc56911338df23694cb4b5c626f02f461c6b68402b2 2307 kissplice_2.6.7-1.dsc c5d538b38055f5c438751807325daaccd3eb878edf30e5dc76762c160b1c8fae 4583195 kissplice_2.6.7.orig.tar.bz2 ef91f98d653cd35a6ea70f9942ec030b4b47157dacc13ad7bff9686360dbed1b 6740 kissplice_2.6.7-1.debian.tar.xz 6b7490f96533b552ff4504a7054d7aba69f003b17975ba396960c39ce157d34f 8966 kissplice_2.6.7-1_source.buildinfo Files: 0fb9f08d3b63321f5b1b68049cae561c 2307 science optional kissplice_2.6.7-1.dsc 23beb6207a4a47f152c88fccc25e2096 4583195 science optional kissplice_2.6.7.orig.tar.bz2 d1a6f5b6332deeb8d682233ce0bd2c19 6740 science optional kissplice_2.6.7-1.debian.tar.xz 8985a85c1c56b24f23f33d5f8791571d 8966 science optional kissplice_2.6.7-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmazk1wACgkQYAMWptwn dHZi/w/+IpY0/DbUKQSeVRA/vBzcX/oeI6utVxSSGOMlW2ecrRkvnr21bOssAUPt le3qOTvhhj1gLUtWxTIYzkYx62aXRMXKW9XUsDEVw44EN5qXp4jyXZTvlsnjUQMa vzdfdvf/YJTrPqQDpQ2S2LjhwqsorzB1jSs12h6jB7fS1DZ0DlU8ZZCXw5NUSYW/ vjEdhHWdSisc4EuVrsc0dR2IBMumnHR08lcCiPf9ARhFaJ9V8iK5cqrFXbt15Z0q nlOR+UfhnnsQUvBnYCCr6ab3eyWQs3qDc3WMB5eyO+h4+ny4bLUQnwPwspn6SZ5a v7C5/y3t2xr7YApyeH2Gxv0jR7WK/WKbgwyubfAXZiVaQ6CxWGmo0p2dGouy7z0O H64hOD4zWMAOhxA8138zGYcrknD3fHuOKWlmTkYhr1e9BURVpWz2CgyMsdC546L0 iDm+UdmEuKurEzL7djXbYiUmoY4pC2GNDJq3zuBw36pqfdYwKl2RhQfmD+J+1jEC +Wqv63yEqoSITUhOU+ufMPga8nGydb53Rt4WIUvEp/FNLEmWe2vrbw/9ZaZBj4k3 o3dlc1xErSLkTaCuxJzOagdSP4uYZxVaja80uvl6fu/dv7a0GD0FIgh7j2XWoU9w kjKDryIXlr2Rnm9zsQr5ELhDKNmnW+mJG/9JMza/IN94J9EE+Rc= =IDD6 -----END PGP SIGNATURE-----
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