Source: kissplice Version: 2.6.7-1 Severity: important Justification: FTBFS Tags: trixie sid ftbfs User: [email protected] Usertags: ftbfs-20250428 ftbfs-trixie ftbfs-randomly
Hi, Your package fails to build randomly on amd64: In the exact same environment, sometimes it builds fine, and sometimes it fails. Relevant part (hopefully): > make[1]: Entering directory > '/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu' > Running tests... > /usr/bin/ctest --force-new-ctest-process --verbose -j8 > UpdateCTestConfiguration from > :/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/DartConfiguration.tcl > UpdateCTestConfiguration from > :/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/DartConfiguration.tcl > Test project /build/reproducible-path/kissplice-2.6.7/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 > Connected to MAKE jobserver > test 1 > Start 1: KisspliceBasicTest > > 1: Test command: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > "-h" > 1: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests > 1: Test timeout computed to be: 10000000 > test 2 > Start 2: KisspliceDBGTest > > 2: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceDBGTest.py > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin" > 2: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests > 2: Test timeout computed to be: 10000000 > test 3 > Start 3: KisspliceTwoSequencesTest > > 3: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceTwoSequencesTest.py > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin" > 3: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests > 3: Test timeout computed to be: 10000000 > test 4 > Start 4: KisspliceGraphAndSequenceTest > > 4: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceGraphAndSequenceTest.py > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin" > 4: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests > 4: Test timeout computed to be: 10000000 > test 5 > Start 5: KisspliceGraphTest > > 5: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/kisspliceGraphTest.py > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin" > 5: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests > 5: Test timeout computed to be: 10000000 > test 6 > Start 6: ksBubbleEnumerationTest > > 6: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/ksBubbleEnumerationTest.py > > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice" > 6: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/functional_tests > 6: Test timeout computed to be: 10000000 > test 7 > Start 7: ksRunModulesTest > > 7: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/ksRunModulesTest.py > > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice" > 7: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/functional_tests > 7: Test timeout computed to be: 10000000 > test 8 > Start 8: ksErrorRemovalTest > > 8: Test command: > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/ksErrorRemovalTest.py > > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice" > 8: Working Directory: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/functional_tests > 8: Test timeout computed to be: 10000000 > 6: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice/ks_bubble_enumeration > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_info_bcc > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_contents_edges_bcc > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_contents_nodes_bcc > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_all_edges_bcc > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_all_nodes_bcc > 2 25 > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_bubble_enumeration_output > 3 bcc_test 0 -u 1000 -L 49 -l 42 -M 10000 -b 5 > 6: b'\t Enumerating bubbles with at most 5 branching nodes in each > path!\n============================================================================\nSummary > of > results\n============================================================================\nNo > of bubbles: > 4\n============================================================================\n' > 6: Ks_Bubble_Enumeration_Test: test SUCCESSFUL > 8: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice/ks_error_removal > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.abundance > > 0.02/build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_error_removal_output > 8: b'252 out of 5336 edges removed\n' > 8: ks_error_removal: test SUCCESSFUL > 7: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/lib/x86_64-linux-gnu/kissplice/ks_run_modules > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.edges > > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/graph_HBM75brainliver_100000_k25.nodes > 25 > /build/reproducible-path/kissplice-2.6.7/tests/functional_tests/data/test_ks_run_modules_output_graph > 1/8 Test #6: ksBubbleEnumerationTest .......... Passed 0.05 sec > 7: 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' > 7: ks_run_modules: test SUCCESSFUL > 2/8 Test #8: ksErrorRemovalTest ............... Passed 0.05 sec > 1: usage: kissplice [-h] [-r READFILES] [-k KVAL] [-b BVAL] [-l LLMAX] > 1: [-m LL_MIN] [-M UL_MAX] [-g GRAPH_PREFIX] [-o OUT_DIR] > 1: [-d PATH_TO_TMP] [-t NBPROCS] [-s OUTPUT_SNPS] [-v] [-u] > 1: [-c MIN_COV] [-C MIN_RELATIVE_COV] [-e MIN_EDIT_DIST] > 1: [-y MAX_CYCLES] [--mismatches MISM] [--mismatchesSNP > MISMSNP] > 1: [--counts COUNTSMETHOD] [--min_overlap MINOVERLAP] > 1: [--timeout TIMEOUT] [--version] [--output-context] > 1: [--output-path] [--output-branch-count] [--keep-bccs] > 1: [--not-experimental] [--max-memory MAX_MEMORY] > 1: [--keep-counts] [--get-mapping-info] [--stranded] > 1: [--strandedAbsoluteThreshold STRANDEDABSOLUTETHRESHOLD] > 1: [--strandedRelativeThreshold STRANDEDRELATIVETHRESHOLD] > 1: [--keep-redundancy] [--keep-low-complexity] > 1: [--lc-entropy-threshold LC_ENT] [--get-redundance-info] > 1: [--get-low-complexity-info] [--type1-only] > 1: > 1: kisSplice - local assembly of SNPs, indels and AS events > 1: > 1: options: > 1: -h, --help show this help message and exit > 1: -r READFILES input fasta/q read files or compressed (.gz) > fasta/q > 1: files (mutiple, such as "-r file1 -r file2...") > 1: -k KVAL k-mer size (default=41) > 1: -b BVAL maximum number of branching nodes (default 5) > 1: -l LLMAX maximal length of the shorter path (default: 2k+1) > 1: -m LL_MIN minimum length of the shorter path (default 2k-8) > 1: -M UL_MAX maximum length of the longest path (default > 1000000), > 1: skipped exons longer than UL_MAX are not reported > 1: -g GRAPH_PREFIX path and prefix to pre-built de Bruijn graph > (suffixed > 1: by .edges/.nodes) if jointly used with -r, graph > used > 1: to find bubbles and reads used for quantification > 1: -o OUT_DIR path to store the results and the summary log file > 1: (default = ./results) > 1: -d PATH_TO_TMP specific directory (absolute path) where to build > 1: temporary files (default temporary directory > 1: otherwise) > 1: -t NBPROCS number of cores (must be <= number of physical > cores) > 1: -s OUTPUT_SNPS 0, 1 or 2. Changes which types of SNPs will be > output. > 1: If 0 (default), will not output SNPs. If 1, will > 1: output Type0a-SNPs. If 2, will output Type0a and > 1: Type0b SNPs (warning: this option may increase a > lot > 1: the running time. You might also want to try the > 1: experimental algorithm here) > 1: -v Verbose mode > 1: -u keep the nodes/edges file for unfinished bccs > 1: -c MIN_COV an integer, k-mers present strictly less than this > 1: number of times in the dataset will be discarded > 1: (default 2) > 1: -C MIN_RELATIVE_COV a percentage from [0,1), edges with relative > coverage > 1: below this number are removed (default 0.05) > 1: -e MIN_EDIT_DIST edit distance threshold, if the two sequences > (paths) > 1: of a bubble have edit distance smaller than this > 1: threshold, the bubble is classified as an inexact > 1: repeat (default 3) > 1: -y MAX_CYCLES maximal number of bubbles enumeration in each bcc. > If > 1: exceeded, no bubble is output for the bcc (default > 1: 100M) > 1: --mismatches MISM Maximal number of substitutions authorized between > a > 1: read and a fragment (for quantification only), > default > 1: 2. If you increase the mismatch and use --counts > think > 1: of increasing min_overlap too. > 1: --mismatchesSNP MISMSNP > 1: Maximal number of substitutions authorized between > a > 1: read and a fragment (for quantification only) for > SNP, > 1: default 0. > 1: --counts COUNTSMETHOD > 1: 0,1 or 2 . Changes how the counts will be > reported. If > 1: 0 : total counts, if 1: counts on junctions, if 2 > 1: (default): all counts. see User guide for more > 1: information > 1: --min_overlap MINOVERLAP > 1: Set how many nt must overlap a junction to be > counted > 1: by --counts option. Default=5. see User guide for > more > 1: information > 1: --timeout TIMEOUT max amount of time (in seconds) spent for > enumerating > 1: bubbles in each bcc. If exceeded, no bubble is > output > 1: for the bcc (default 100000) > 1: --version show program's version number and exit > 1: --output-context Will output the maximum non-ambiguous context of a > 1: bubble > 1: --output-path Will output the id of the nodes composing the two > 1: paths of the bubbles. > 1: --output-branch-count > 1: Will output the number of branching nodes in each > 1: path. > 1: --keep-bccs Keep the node/edges files for all bccs. > 1: --not-experimental Do not use a new experimental algorithm that > searches > 1: for bubbles by listing all paths. > 1: --max-memory MAX_MEMORY > 1: If you use the experimental algorithm, you must > 1: provide the maximum size of the process's virtual > 1: memory (address space) in megabytes (default > 1: unlimited). WARNING: this option does not work on > Mac > 1: operating systems. > 1: --keep-counts Keep the .counts file after the sequencing-errors- > 1: removal step. > 1: --get-mapping-info Creates a file with the KissReads mapping > information > 1: of the reads on the bubbles. > 1: --stranded Execute kissreads in stranded mode. > 1: --strandedAbsoluteThreshold STRANDEDABSOLUTETHRESHOLD > 1: Sets the minimum number of reads mapping to a path > of > 1: a bubble in a read set is needed to call a strand. > 1: --strandedRelativeThreshold STRANDEDRELATIVETHRESHOLD > 1: If a strand is called for a path of a bubble in a > read > 1: set, but the proportion of reads calling this > strand > 1: is less than this threshold, then the strand of the > 1: path is set to '?' (any strand - not enough > evidence > 1: to call a strand). > 1: --keep-redundancy Keep the Type_1 redundant cycles in the result > file. > 1: --keep-low-complexity > 1: Keep the low-complexity Type_1 cycles in the result > 1: file. > 1: --lc-entropy-threshold LC_ENT > 1: Cycles with a Shannon entropy value for their upper > 1: path below this value will be removed (use > --keep-low- > 1: complexity to keep them). > 1: --get-redundance-info > 1: Creates files with informations on compressed > 1: redundant cycles. > 1: --get-low-complexity-info > 1: Creates a file with informations on removed low- > 1: complexity cycles. > 1: --type1-only Only quantify Type 1 bubbles (alternative splicing > 1: events, MAJOR SPEED UP with -b > 10 BUT all other > 1: bubbles will not appear in the result file). > 3/8 Test #7: ksRunModulesTest ................. Passed 0.06 sec > 4/8 Test #1: KisspliceBasicTest ............... Passed 0.07 sec > 3: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta > -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta > -C 0 > 3: Integration test error : b'Traceback (most recent call last):\n File > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice", > line 1665, in <module>\n main()\n ~~~~^^\n File > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice", > line 1412, in main\n os.mkdir(outdir)\n > ~~~~~~~~^^^^^^^^\nFileExistsError: [Errno 17] File exists: \'results\'\n' > 5/8 Test #3: KisspliceTwoSequencesTest ........***Failed Required regular > expression not found. Regex=[test SUCCESSFUL > ] 0.11 sec > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta > -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75liver_100000.fasta > -C 0 > Integration test error : b'Traceback (most recent call last):\n File > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice", > line 1665, in <module>\n main()\n ~~~~^^\n File > "/build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice", > line 1412, in main\n os.mkdir(outdir)\n > ~~~~~~~~^^^^^^^^\nFileExistsError: [Errno 17] File exists: \'results\'\n' > > 5: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -g > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -C 0 > 5: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -g > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -C 0\nUsing the read files: None\nResults will be stored in: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results\nSummary > log file will be saved in: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-04-29_01-57-45_840661\n\n\nElapsed > time: 0.0 seconds\n\n[01:57:45 29/04/2025] --> Finding the > BCCs...\n[01:57:45 29/04/2025] --> Done!\nElapsed time: 0.0 > seconds\n\n[01:57:45 29/04/2025] --> Enumerating all bubbles...\nTotal number > of bubbles found: 57.0\n[01:57:45 29/04/2025] --> Done!\nElapsed time: 0.3 > seconds\n\n[01:57:45 29/04/2025] --> Starting Bubble Output Module\n[01:57:45 > 29/04/2025] --> Sampling bubbles by type...\n[01:57:45 29/04/2025] --> > Done!\nYou can now access all bubbles without read coherency in: > results\n\n[01:57:45 29/04/2025] --> Removing low-complexity/redundant > bubbles...\n[01:57:45 29/04/2025] --> Done!\nElapsed time: 0.0 > seconds\nElapsed time: 0.0 seconds\n\n\n\n \t\t ******** We are done, final > results are in files > results/results_graph_HBM75brain_100000_HBM75liver_100000_k25_type_*.fa > **********\n\t\t TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or > sequencing substitution errors, 83 found\n\t\t\t 0b: Multiple SNPs, Inexact > Repeats or sequencing substitution errors, 17 found\n\t\t\t 1: Alternative > Splicing Events, 1 found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t > 3: Short Indels (<3nt), 16 found\n\t\t\t 4: All others, composed by a shorter > path of length > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of > the execution can be found in the log file: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-04-29_01-57-45_840661**********\n' > 5: kisspliceGraphTest.py: test SUCCESSFUL > 6/8 Test #5: KisspliceGraphTest ............... Passed 0.41 sec > 4: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -g > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta > -C 0 > 4: b'\nThis is KisSplice, version 2.6.7\n\nThe command line was: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/bin/kissplice > -s 2 -k 25 -M 1000 -g > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/graph_HBM75brain_100000_HBM75liver_100000_k25 > -r > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta > -C 0\n-r and -g options used together: \nthe graph will be used to find > events, while reads files are used for checking read-coherency and > coverage\nUsing the read files: > /build/reproducible-path/kissplice-2.6.7/tests/integration_tests/data/HBM75brain_100000.fasta\nResults > will be stored in: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results\nSummary > log file will be saved in: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-04-29_01-57-45_663012\n\n\nElapsed > time: 0.0 seconds\n\n[01:57:45 29/04/2025] --> Finding the > BCCs...\n[01:57:45 29/04/2025] --> Done!\nElapsed time: 0.0 > seconds\n\n[01:57:45 29/04/2025] --> Enumerating all bubbles...\nTotal number > of bubbles found: 57.0\n[01:57:45 29/04/2025] --> Done!\nElapsed time: 0.3 > seconds\n\n[01:57:45 29/04/2025] --> Starting Bubble Output Module\nBefore > checking for read coherency, all bubbles will be written to folder > results/results_without_read_coherency\nThis enables you to access them even > before the read coherency module finishes, which can take a long > time\n[01:57:45 29/04/2025] --> Sampling bubbles by type...\n[01:57:45 > 29/04/2025] --> Done!\nYou can now access all bubbles without read coherency > in: results/results_without_read_coherency\n\n[01:57:45 29/04/2025] --> > Removing low-complexity/redundant bubbles...\n[01:57:45 29/04/2025] --> > Done!\nElapsed time: 0.0 seconds\n\n[01:57:45 29/04/2025] --> Computing read > coherence and coverage...\n[01:57:45 29/04/2025] --> Done!\n[01:57:45 > 29/04/2025] --> Sorting all bubbles...\n[01:57:45 29/04/2025] --> > Done!\nElapsed time: 0.4 seconds\n\n\n\n \t\t ******** We are done, final > coherent results are in files > results/results_HBM75brain_100000_k25_coherents_type_*.fa ********** \n \t\t > ******** All non read coherent results are in files > results/results_HBM75brain_100000_k25_uncoherent.fa ****** \n\n\n\t\t > TYPES:\n\t\t\t 0a: Single SNPs, Inexact Repeats or sequencing substitution > errors, 19 found\n\t\t\t 0b: Multiple SNPs, Inexact Repeats or sequencing > substitution errors, 1 found\n\t\t\t 1: Alternative Splicing Events, 0 > found\n\t\t\t 2: Inexact Tandem Repeats, 0 found\n\t\t\t 3: Short Indels > (<3nt), 14 found\n\t\t\t 4: All others, composed by a shorter path of length > > 2k not being a SNP, 0 found\n\n\n \t\t ******** A summary of the execution > can be found in the log file: > /build/reproducible-path/kissplice-2.6.7/obj-x86_64-linux-gnu/tests/integration_tests/results/kissplice_log_summary_2025-04-29_01-57-45_663012**********\n' > 4: kisspliceGraphAndSequenceTest.py: test SUCCESSFUL > 7/8 Test #4: KisspliceGraphAndSequenceTest .... Passed 0.79 sec > 8/8 Test #2: KisspliceDBGTest ................. Passed 3.83 sec > > 88% tests passed, 1 tests failed out of 8 > > Total Test time (real) = 3.83 sec > > The following tests FAILED: > 3 - KisspliceTwoSequencesTest (Failed) > Errors while running CTest > make[1]: *** [Makefile:74: test] Error 8 > make[1]: Leaving directory > '/build/reproducible-path/kissplice-2.6.7/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/2025/04/28/kissplice_2.6.7-1_unstable.log You can find other build logs (including successful ones) in: http://qa-logs.debian.net/2025/04/28/ All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20250428;[email protected] or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250428&[email protected]&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.
