Hi Sascha, On Sun, Jun 21, 2020 at 10:03:49PM +0200, Lucas Nussbaum wrote: > > ====================================================================== > > ERROR: test filter_mummer_variants > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 96, in test_filter_mummer_variants > > v1 = > > pymummer.variant.Variant(pymummer.snp.Snp('4\tC\tT\t4\tx\tx\t39\t39\tx\tx\tgene\tcontig')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 4 C T 4 x x 39 39 x x > > gene contig > > > > ====================================================================== > > ERROR: test _get_variant_effect > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 55, in test_get_variant_effect > > v1 = > > pymummer.variant.Variant(pymummer.snp.Snp('6\tC\tT\t6\tx\tx\t39\t39\tx\tx\tgene\tcontig')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 6 C T 6 x x 39 39 x x > > gene contig > > > > ====================================================================== > > ERROR: test get_variants presence absence genes > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 309, in test_get_variants_presence_absence > > v2 = > > pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig1')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 14 C A 14 x x 42 42 x x > > presence_absence contig1 > > > > ====================================================================== > > ERROR: test get_variants variants only > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 357, in test_get_variants_variants_only > > v2 = > > pymummer.variant.Variant(pymummer.snp.Snp('14\tC\tA\t14\tx\tx\t42\t42\tx\tx\tvariants_only\tcontig1')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 14 C A 14 x x 42 42 x x > > variants_only contig1 > > > > ====================================================================== > > ERROR: test _get_one_variant_for_one_contig_coding > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 156, in test_one_var_one_ctg_cdg > > v0 = > > pymummer.variant.Variant(pymummer.snp.Snp('6\tT\tA\t6\tx\tx\t42\t42\tx\tx\tpresence_absence\tcontig')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 6 T A 6 x x 42 42 x x > > presence_absence contig > > > > ====================================================================== > > ERROR: test _get_one_variant_for_one_contig_non_coding > > ---------------------------------------------------------------------- > > Traceback (most recent call last): > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 21, in > > __init__ > > self.reverse = {'1': False, '-1': True}[l[-3]] > > KeyError: 'x' > > > > During handling of the above exception, another exception occurred: > > > > Traceback (most recent call last): > > File > > "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py", > > line 113, in test_one_var_one_ctg_noncdg > > v0 = > > pymummer.variant.Variant(pymummer.snp.Snp('2\tT\tA\t2\tx\tx\t42\t42\tx\tx\tnon_coding\tcontig')) > > File "/usr/lib/python3/dist-packages/pymummer/snp.py", line 25, in > > __init__ > > raise Error('Error constructing pymummer.snp.Snp from mummer show-snps > > output at this line:\n' + line) > > pymummer.snp.Error: Error constructing pymummer.snp.Snp from mummer > > show-snps output at this line: > > 2 T A 2 x x 42 42 x x > > non_coding contig > > > > ---------------------------------------------------------------------- > > Ran 356 tests in 57.387s > > > > FAILED (SKIP=2, errors=6) > > E: pybuild pybuild:352: test: plugin distutils failed with: exit code=1: cd > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.8_ariba/build; python3.8 -m nose -v > > dh_auto_test: error: pybuild --test --test-nose -i python{version} -p 3.8 > > returned exit code 13
It seems the test failures are all connected to pymummer which was upgraded recently. BTW, I've added a (Build-)Depends on spades which also shows up in the test log as missing without causing an actual error. Kind regards Andreas. -- http://fam-tille.de