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