[Debian-med-packaging] Bug#1104392: kissplice: FTBFS randomly: dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit code 2
Lucas Nussbaum
lucas at debian.org
Tue Apr 29 14:48:13 BST 2025
Source: kissplice
Version: 2.6.7-1
Severity: important
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
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;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20250428&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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