Public bug reported: Imported from Debian bug http://bugs.debian.org/1074658:
Source: kissplice Version: 2.6.2-3 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-20240702 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > The following tests FAILED: > 3 - KisspliceDBGTest (Failed) > 4 - KisspliceTwoSequencesTest (Failed) > 5 - KisspliceGraphAndSequenceTest (Failed) > 6 - KisspliceGraphTest (Failed) > Errors while running CTest ** Affects: kissplice (Ubuntu) Importance: High Status: Triaged ** Affects: kissplice (Debian) Importance: Undecided Status: New ** Tags: update-excuse ** Bug watch added: Debian Bug tracker #1074658 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1074658 ** Changed in: kissplice (Debian) Remote watch: None => Debian Bug tracker #1074658 ** Description changed: Imported from Debian bug http://bugs.debian.org/1074658: Source: kissplice Version: 2.6.2-3 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: [email protected] 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/k [...] + > The following tests FAILED: + > 3 - KisspliceDBGTest (Failed) + > 4 - KisspliceTwoSequencesTest (Failed) + > 5 - KisspliceGraphAndSequenceTest (Failed) + > 6 - KisspliceGraphTest (Failed) + > Errors while running CTest ** Changed in: kissplice (Ubuntu) Importance: Undecided => High ** Tags added: update-excuse ** Changed in: kissplice (Ubuntu) Status: New => Triaged -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2075171 Title: kissplice: FTBFS: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit code 2 To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/kissplice/+bug/2075171/+subscriptions -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
