Your message dated Wed, 30 Apr 2025 20:34:47 +0000
with message-id <[email protected]>
and subject line Bug#1104392: fixed in kissplice 2.6.7-2
has caused the Debian Bug report #1104392,
regarding kissplice: FTBFS randomly: dh_auto_test: error: cd
obj-x86_64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 returned exit
code 2
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1104392: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1104392
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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.
--- End Message ---
--- Begin Message ---
Source: kissplice
Source-Version: 2.6.7-2
Done: Étienne Mollier <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kissplice, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <[email protected]> (supplier of updated kissplice package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 30 Apr 2025 21:27:51 +0200
Source: kissplice
Architecture: source
Version: 2.6.7-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Étienne Mollier <[email protected]>
Closes: 1104392
Changes:
kissplice (2.6.7-2) unstable; urgency=medium
.
* Team upload.
* d/rules: make tests sequential. (Closes: #1104392)
* d/control: declare compliance to standards version 4.7.2.
* tests-2to3.patch: normalize Last-Update timestamp.
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