Error running test_rmats script using conda env

Hi,

I've installed rMATS using python/2.7.16 and did not see any errors while running the build script. When I run the ./test_rmats script, all of the tests fail. I've pasted the complete output from running ./test_rmats below. Can you help me to troubleshoot?

Thank you very much for your help, George

[gtollefs@login005 rmats-turbo-master]$ ./test_rmats WARNING: A conda environment already exists at '/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/test_rmats' Remove existing environment (y/[n])? n

CondaSystemExit: Exiting.

Collecting package metadata (current_repodata.json): done Solving environment: done

All requested packages already installed.

test (tests.allow_clipping.test.ClippingAllowedTest) ... FAIL test (tests.allow_clipping.test.ClippingNotAllowedTest) ... FAIL test (tests.alternative_3_splice_site_novel.test.NovelJunction) ... FAIL test (tests.alternative_3_splice_site_novel.test.NovelSpliceSite) ... FAIL test (tests.alternative_5_splice_site_novel.test.NovelJunction) ... FAIL test (tests.alternative_5_splice_site_novel.test.NovelSpliceSite) ... FAIL test (tests.fixed_event_set.test.Test) ... FAIL test (tests.mutually_exclusive_exons_novel.test.NovelJunction) ... FAIL test (tests.mutually_exclusive_exons_novel.test.NovelSpliceSite) ... FAIL test (tests.only_one_sample.test.StatOffTest) ... FAIL test (tests.only_one_sample.test.StatOnTest) ... FAIL test (tests.overlapped_gene.test.Test) ... FAIL test (tests.paired_stats.test.FilteredEventTest) ... FAIL test (tests.paired_stats.test.OneEventTest) ... FAIL test (tests.paired_stats.test.TwoEventTest) ... FAIL test (tests.prep_post.test.Test) ... FAIL test (tests.retained_intron_novel.test.NovelJunction) ... FAIL test (tests.retained_intron_novel.test.NovelSpliceSite) ... FAIL test (tests.skipped_exon_basic.test.Test) ... FAIL test (tests.skipped_exon_novel.test.NovelJunction) ... FAIL test (tests.skipped_exon_novel.test.NovelSpliceSite) ... FAIL test (tests.skipped_exon_novel.test.NovelSpliceSiteNotNovelJunction) ... FAIL test (tests.stranded.test.FirstStrandTest) ... FAIL test (tests.stranded.test.SecondStrandTest) ... FAIL test (tests.stranded.test.UnstrandedTest) ... FAIL test (tests.task_stat.test.Test) ... FAIL test (tests.variable_read_length.test.Length1Test) ... FAIL test (tests.variable_read_length.test.Length1VariableTest) ... FAIL test (tests.variable_read_length.test.Length2Test) ... FAIL test (tests.variable_read_length.test.Length2VariableTest) ... FAIL test (tests.variable_read_length.test.NoLengthTest) ... FAIL

====================================================================== FAIL: test (tests.allow_clipping.test.ClippingAllowedTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/allow_clipping/test.py", line 160, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/allow_clipping/test.py", line 168, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.allow_clipping.test.ClippingNotAllowedTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/allow_clipping/test.py", line 188, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/allow_clipping/test.py", line 191, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.alternative_3_splice_site_novel.test.NovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_3_splice_site_novel/test.py", line 95, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_3_splice_site_novel/test.py", line 114, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.alternative_3_splice_site_novel.test.NovelSpliceSite)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_3_splice_site_novel/test.py", line 156, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_3_splice_site_novel/test.py", line 180, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.alternative_5_splice_site_novel.test.NovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_5_splice_site_novel/test.py", line 95, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_5_splice_site_novel/test.py", line 114, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.alternative_5_splice_site_novel.test.NovelSpliceSite)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_5_splice_site_novel/test.py", line 156, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/alternative_5_splice_site_novel/test.py", line 180, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.fixed_event_set.test.Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/fixed_event_set/test.py", line 64, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/fixed_event_set/test.py", line 332, in _check_results self._check_results_original() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/fixed_event_set/test.py", line 339, in _check_results_original self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.mutually_exclusive_exons_novel.test.NovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/mutually_exclusive_exons_novel/test.py", line 99, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/mutually_exclusive_exons_novel/test.py", line 136, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.mutually_exclusive_exons_novel.test.NovelSpliceSite)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/mutually_exclusive_exons_novel/test.py", line 194, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/mutually_exclusive_exons_novel/test.py", line 224, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.only_one_sample.test.StatOffTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/only_one_sample/test.py", line 171, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/only_one_sample/test.py", line 179, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.only_one_sample.test.StatOnTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/only_one_sample/test.py", line 148, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/only_one_sample/test.py", line 151, in _check_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.overlapped_gene.test.Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/overlapped_gene/test.py", line 45, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/overlapped_gene/test.py", line 109, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.paired_stats.test.FilteredEventTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 314, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 373, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.paired_stats.test.OneEventTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 156, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 199, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.paired_stats.test.TwoEventTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 229, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/paired_stats/test.py", line 280, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.prep_post.test.Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/prep_post/test.py", line 89, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/prep_post/test.py", line 409, in _check_results self._check_results_prep_1() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/prep_post/test.py", line 441, in _check_results_prep_1 self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.retained_intron_novel.test.NovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/retained_intron_novel/test.py", line 95, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/retained_intron_novel/test.py", line 115, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.retained_intron_novel.test.NovelSpliceSite)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/retained_intron_novel/test.py", line 152, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/retained_intron_novel/test.py", line 172, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.skipped_exon_basic.test.Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_basic/test.py", line 49, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_basic/test.py", line 164, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 96, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 115, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelSpliceSite)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 160, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 191, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelSpliceSiteNotNovelJunction)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 255, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/test.py", line 278, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.stranded.test.FirstStrandTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 148, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 156, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.stranded.test.SecondStrandTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 198, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 206, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.stranded.test.UnstrandedTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 248, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/stranded/test.py", line 256, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.task_stat.test.Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/task_stat/test.py", line 68, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/task_stat/test.py", line 244, in _check_results self._check_results_statoff() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/task_stat/test.py", line 267, in _check_results_statoff self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.variable_read_length.test.Length1Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 201, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 212, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.variable_read_length.test.Length1VariableTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 251, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 263, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.variable_read_length.test.Length2Test)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 324, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 335, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.variable_read_length.test.Length2VariableTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 374, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 386, in _check_results self._check_no_error_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 61, in _check_no_error_results self.assertEqual(self._rmats_return_code, 0) AssertionError: 1 != 0

====================================================================== FAIL: test (tests.variable_read_length.test.NoLengthTest)

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 447, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 456, in _check_results tests.util.assert_some_line_has(self, err_lines, File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/util.py", line 41, in assert_some_line_has test.fail('{} not found in any line:\n{}'.format(string, lines)) AssertionError: --readLength is required not found in any line: ['Traceback (most recent call last):\n', ' File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py", line 19, in \n', ' from rmatspipeline import run_pipe\n', 'ImportError: No module named rmatspipeline\n']

Ran 31 tests in 21.664s

FAILED (failures=31) [gtollefs@login005 rmats-turbo-master]$

The output that gets printed when running ./test_rmats shows which tests failed, but it doesn't always show a useful error message. You can look in the tests/ directory for more details. As an example the failed test named tests.variable_read_length.test.NoLengthTest should have an error message in tests/variable_read_length/no_length/command_output/

The error message that was printed for that test looks like:

Traceback (most recent call last):
File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py", line 19, in
from rmatspipeline import run_pipe
ImportError: No module named rmatspipeline

The test should try to call rmats using the run_rmats script and use this command: https://github.com/Xinglab/rmats-turbo/blob/ab7dbf625005e3dd3399c01cac93a8c5072c5a11/run_rmats#L19

It might be that it is finding the wrong version of python. Can you reproduce the error by manually running python /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py? You could try editing that line of the run_rmats script to use an absolute /path/to/python to ensure that it gets the right version

If you still get that error even with the full python path, then there might have been a build error. There should be a file like rmatspipeline.so or rmatspipeline.cpython-36m-x86_64-linux-gnu.so in the rmats-turbo directory if the build was successful. If not, could you try running the build with a fresh copy of the source code and posting the output?

Hi @EricKutschera,

Thank you very much for your quick reply. I have reproduced the error by running python /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py. The output is:

[gtollefs@login006 rmats-turbo-master]$ python /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py", line 19, in from rmatspipeline import run_pipe ImportError: No module named rmatspipeline

I tried replacing python with the our full python path to python/2.7.16 which is /bin/python2.7 in the run_rmats script and got the same error. I then tried replacing python with the full path in the /rmats-turbo-master/rmats.py script and still got the same error. I realized

I do see the rmatspipeline.cpython-36m-x86_64-linux-gnu.so in my directory.

I also noticed that, when calling /bin/python2.7, the GCC version printed to the display is older than the required GCC version in the rMATS dependencies (from the docs:GCC (>=5.4.0) ). I gcc/10.2 loaded as a module on our computing cluster, but I wonder if python2.7 automatically loads gcc/4.8.5 and if this could be causing any issues. Though, I don't see an output message saying gcc/10.2 has been unloaded.

Edit: I checked the stderr output of the other failed tests and the error message is the same in the four that I checked:

[gtollefs@login006 command_output]$ pwd /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/skipped_exon_novel/nss_not_nj/command_output [gtollefs@login006 command_output]$ more rmats_stderr Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py", line 19, in from rmatspipeline import run_pipe ImportError: No module named rmatspipeline

rmatspipeline.cpython-36m-x86_64-linux-gnu.so indicates that rmats was built with python3 (it should be just rmatspipeline.so for python2). Maybe something about your environment was different when you ran ./build_rmats that caused it to find python3. Can you try running rmats.py with an absolute path to python3?

rmatspipeline.cpython-36m-x86_64-linux-gnu.so indicates that rmats was built with python3 (it should be just rmatspipeline.so for python2). Maybe something about your environment was different when you ran ./build_rmats that caused it to find python3. Can you try running rmats.py with an absolute path to python3?

Strange, I'm pretty sure that I had python2 loaded. I tried running rmats.py with the absolute path to python3 and received the same error. I removed the whole rMATS directory and am building it again in a fresh session with python 2.7.16 loaded. I saw a message during the build saying that python 3.6.12 was used. I've pasted that snippet as well as the complete build output below. It looks like for some reason, python 3.6.12 is being used in the conda env build even though I haven't loaded python/3.6.12. Maybe conda automatically uses 3.6.12 on my shared computing system. I think we're getting closer to the solution.

Most relevant snippet:

## Package Plan ##

environment location: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats

added / updated specs:

cython==0.29.21

numpy==1.16.6

python==3.6.12

The following packages will be downloaded:\

...

The complete text of the commands and output:

[gtollefs@login005 rmats-turbo-master]$ module load python/2.7.16 blas lapack gsl/2.5 gcc/10.2 cmake/3.15.4 samtools star module: unloading 'python/3.5.2' module: loading 'python/2.7.16' module: unloading 'blas/3.7.0' module: loading 'blas/3.7.0' module: unloading 'lapack/3.7.0' module: loading 'lapack/3.7.0' module: unloading 'gsl/2.5' module: loading 'gsl/2.5' module: unloading 'gcc/10.2' module: loading 'gcc/10.2' module: gcc: "Note: loading the gcc module overrides the gcc version on the system. If you want to revert to the version of gcc provided by the OS, unload the gcc module." module: unloading 'cmake/3.15.4' module: loading 'cmake/3.15.4' module: unloading 'samtools/1.9' module: loading 'samtools/1.9' module: unloading 'star/2.6.1b' module: loading 'star/2.6.1b' [gtollefs@login005 rmats-turbo-master]$ ./build_rmats --conda --no-paired-model Collecting package metadata (current_repodata.json): done Solving environment: done

## Package Plan ##

environment location: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats

Proceed ([y]/n)?

Preparing transaction: done Verifying transaction: done Executing transaction: done # # To activate this environment, use # # $ conda activate /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats # # To deactivate an active environment, use # # $ conda deactivate

Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): / done Solving environment: done

## Package Plan ##

environment location: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats

added / updated specs:

cython==0.29.21

numpy==1.16.6

python==3.6.12

The following packages will be downloaded:
package                    |            build
---------------------------|-----------------
setuptools-58.0.3          |   py36h5fab9bb_0         934 KB  conda-forge
------------------------------------------------------------
                                       Total:         934 KB
The following NEW packages will be INSTALLED:

_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-1_gnu ca-certificates conda-forge/linux-64::ca-certificates-2021.5.30-ha878542_0 cython conda-forge/linux-64::cython-0.29.21-py36hc4f0c31_2 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.36.1-hea4e1c9_2 libblas conda-forge/linux-64::libblas-3.9.0-11_linux64_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-11_linux64_openblas libffi conda-forge/linux-64::libffi-3.3-h58526e2_2 libgcc-ng conda-forge/linux-64::libgcc-ng-11.1.0-hc902ee8_8 libgfortran-ng conda-forge/linux-64::libgfortran-ng-11.1.0-h69a702a_8 libgfortran5 conda-forge/linux-64::libgfortran5-11.1.0-h6c583b3_8 libgomp conda-forge/linux-64::libgomp-11.1.0-hc902ee8_8 liblapack conda-forge/linux-64::liblapack-3.9.0-11_linux64_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.17-pthreads_h8fe5266_1 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-11.1.0-h56837e0_8 ncurses conda-forge/linux-64::ncurses-6.2-h58526e2_4 numpy conda-forge/linux-64::numpy-1.16.6-py36h2aa4a07_0 openssl conda-forge/linux-64::openssl-1.1.1l-h7f98852_0 pip conda-forge/noarch::pip-21.2.4-pyhd8ed1ab_0 python conda-forge/linux-64::python-3.6.12-hffdb5ce_0_cpython python_abi conda-forge/linux-64::python_abi-3.6-2_cp36m readline conda-forge/linux-64::readline-8.1-h46c0cb4_0 setuptools conda-forge/linux-64::setuptools-58.0.3-py36h5fab9bb_0 sqlite conda-forge/linux-64::sqlite-3.36.0-h9cd32fc_0 tk conda-forge/linux-64::tk-8.6.11-h27826a3_1 wheel conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1 xz conda-forge/linux-64::xz-5.2.5-h516909a_1 zlib conda-forge/linux-64::zlib-1.2.11-h516909a_1010

Proceed ([y]/n)?

Downloading and Extracting Packages setuptools-58.0.3 | 934 KB | ############################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done cd bamtools; mkdir -p build; cd build; cmake ..; make; -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Configuring done -- Generating done -- Build files have been written to: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build make[1]: Entering directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' make[2]: Entering directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' make[3]: Entering directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' Scanning dependencies of target SharedHeaders make[3]: Leaving directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' make[3]: Entering directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' make[3]: Leaving directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' [ 0%] Built target SharedHeaders make[3]: Entering directory 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Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_convert.cpp.o [ 87%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o [ 88%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o [ 89%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o [ 90%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o [ 91%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o [ 92%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o [ 93%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o [ 94%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o [ 95%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o [ 96%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o [ 97%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o [ 98%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o [ 99%] Building CXX object src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o [100%] Linking CXX executable ../../../bin/bamtools make[3]: Leaving directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' [100%] Built target bamtools_cmd make[2]: Leaving directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' make[1]: Leaving directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/build' cd bamtools/lib; rm .so .so. .dylib rm: cannot remove ‘.dylib’: No such file or directory make: [build] Error 1 (ignored) cd rMATS_C; make; make[1]: Entering directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C' cd lbfgs_scipy && make make[2]: Entering directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C/lbfgs_scipy' gfortran -c -O2 -c -o lbfgsb.o lbfgsb.f gfortran -c -O2 -c -o linpack.o linpack.f gfortran -c -O2 -c -o timer.o timer.f make[2]: Leaving directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C/lbfgs_scipy' cc -I/gpfs/runtime/opt/gsl/2.5/include -Wall -O2 -msse2 -funroll-loops -fopenmp -o rMATSexe src/main.c src/myfunc.c src/util.c src/cthreadpool.c lbfgs_scipy/lbfgsb.o lbfgs_scipy/linpack.o lbfgs_scipy/timer.o -L/gpfs/runtime/opt/gsl/2.5/lib -lgsl -lgslcblas -lm -lm -lgfortran -lgsl -lgslcblas -lgomp -lblas -llapack make clean make[2]: Entering directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C' rm -rf util.o myfunc.o cthreadpool.o .o src/.o lbfgs_scipy/.o rm -rf rMATS.Rcheck make[2]: Leaving directory /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C' make[1]: Leaving directory/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rMATS_C' cd rMATS_pipeline; python setup.py build_ext; Compiling rmatspipeline/rmatspipeline.pyx because it changed. [1/1] Cythonizing rmatspipeline/rmatspipeline.pyx running build_ext building 'rmats.rmatspipeline' extension creating build creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/rmatspipeline gcc -pthread -B /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/include -I/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats/include/python3.6m -c rmatspipeline/rmatspipeline.cpp -o build/temp.linux-x86_64-3.6/rmatspipeline/rmatspipeline.o -O3 -funroll-loops -std=c++11 -fopenmp -DSTDC_CONSTANT_MACROS -DSTDC_LIMIT_MACROS -w -Wl,-static cc1plus: warning: command-line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/rmats g++ -pthread -shared -B /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats/compiler_compat -L/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats/lib -Wl,-rpath=/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/conda_envs/rmats/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/rmatspipeline/rmatspipeline.o -L/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/bamtools/lib -lm -lstdc++ -lbamtools -lz -o build/lib.linux-x86_64-3.6/rmats/rmatspipeline.cpython-36m-x86_64-linux-gnu.so -lbamtools -lm -std=c++11 -lz -fopenmp cp find ./rMATS_pipeline/build | grep so .; [gtollefs@login005 rmats-turbo-master]$

Interestingly, module python/3.6.12 is not installed as a module on my system. I tried adding the absolute path to python/3.6.6 (the closest release) to the run_rmats script but got the following error:

[gtollefs@login005 rmats-turbo-master]$ python3 rmats.py Traceback (most recent call last): File "rmats.py", line 19, in from rmatspipeline import run_pipe ImportError: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmatspipeline.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZNK8BamTools12BamAlignment14SetErrorStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8

When I activate the conda environment first (which I presume isn't necessary to do explicitly), I get the same error message:

_envs/rmats) [gtollefs@login005 rmats-turbo-master]$ python rmats.py Traceback (most recent call last): File "rmats.py", line 19, in from rmatspipeline import run_pipe ImportError: /gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmatspipeline.cpython-36m-x86_64-linux-gnu.so: undefined symbol: _ZNK8BamTools12BamAlignment14SetErrorStringERKNSt7__cxx1112basic_stringIcSt11chartraitsIcESaIcEEES8

Lastly, I searched online for similar error messages and see the cause may be that the gfortran library present during installation isn't available while running. I actually did need to run export FC=gfortran in order for the build script to see my installation of gfortran. Even though I've run export FC=gfortran in the session in which I am running the rmats.py script, maybe the script doesn't see the FC environment variable?

If you run ./build_rmats --conda then it will create a conda environment for running the build and also for running rmats once the build completes. That conda environment includes python3.6. With --conda it shouldn't matter what python module you have loaded. You can use run_rmats which will activate the conda environment before running rmats.py https://github.com/Xinglab/rmats-turbo/blob/ab7dbf625005e3dd3399c01cac93a8c5072c5a11/run_rmats#L11

The error undefined symbol: ZNK8BamTools12BamAlignment14SetErrorStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8 looks like it is the same issue as https://github.com/Xinglab/rmats-turbo/issues/21

Your build log shows that it found these compilers when building bamtools:

Check for working C compiler: /usr/bin/cc
Check for working CXX compiler: /usr/bin/c++

Later in the build log when it builds rmatspipeline it uses gcc and g++ without a full path. You should be able to get the build to consistently find the same compilers by setting the CC and CXX environment variables similar to what you did for the FC environment variable. There is a place for this in a script that the build uses: https://github.com/Xinglab/rmats-turbo/blob/8b168116c1594d7e02d764ae14a5ef28dbf38de1/setup_environment.sh#L28

Thank you very much @EricKutschera, I'm working with my system admins to identify the path to gcc and g++ on our system so that I can try setting them in my working environment and then will rerun the setup script. Would you recommend removing the current build and running it again, or is it ok to overwrite by running the setup script again?

In this case I think you will need to remove the current build and start over because the individual build results were created successfully, but with incompatible compiler versions. If the build files are not removed then some steps of the build may see the old build results and use them

Ok, thank you very much. I'll remove the current build and will report back if I'm able to install and test successfully, bearing in mind that some tests will fail because I am not building with the paired model.

Hi @EricKutschera

I've rebuild rMATS by removing the previous build and rebuilding after uncommenting the three lines in the setup_environment.sh script which find the module env paths.

This time when I run rmats.py I get a message asking for bam file input which is promising (see below.)

[gtollefs@login005 rmats-turbo-master]$ python3 rmats.py ERROR: BAM/FASTQ required. Please check b1, b2, s1 and s2.

However when I run ./test_rmats all of the tests fail. I've pasted the output of one of the test logs below:

Traceback (most recent call last): File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 447, in test self._run_test() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/base_test.py", line 17, in _run_test self._check_results() File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/variable_read_length/test.py", line 456, in _check_results tests.util.assert_some_line_has(self, err_lines, File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/tests/util.py", line 41, in assert_some_line_has test.fail('{} not found in any line:\n{}'.format(string, lines)) AssertionError: --readLength is required not found in any line: ['Traceback (most recent call last):\n', ' File "/gpfs/data/dgamsiz/Uzun_Lab/gtollefs/tpp1_splicing_project/rMATS/rmats-turbo-master/rmats.py", line 19, in \n', ' from rmatspipeline import run_pipe\n', 'ImportError: No module named rmatspipeline\n']

I built rMATS using the --no_paired_model parameter, so I expected some of the tests to fail, but not all of them.

This is the same error from earlier: ImportError: No module named rmatspipeline

Since you didn't see that error when running with python3 rmats.py, I think the build did successfully produce a file like rmatspipeline.cpython-36m-x86_64-linux-gnu.so. You could try setting an absolute path to python 3 in run_rmats

Hi @EricKutschera, that solved it! I set the absolute path to python 3 and it produced results without error. Thank you very much for all of your help.

George

Xinglab / rmats-turbo

Error running test_rmats script using conda env #146

All requested packages already installed.

====================================================================== FAIL: test (tests.allow_clipping.test.ClippingAllowedTest)

====================================================================== FAIL: test (tests.allow_clipping.test.ClippingNotAllowedTest)

====================================================================== FAIL: test (tests.alternative_3_splice_site_novel.test.NovelJunction)

====================================================================== FAIL: test (tests.alternative_3_splice_site_novel.test.NovelSpliceSite)

====================================================================== FAIL: test (tests.alternative_5_splice_site_novel.test.NovelJunction)

====================================================================== FAIL: test (tests.alternative_5_splice_site_novel.test.NovelSpliceSite)

====================================================================== FAIL: test (tests.fixed_event_set.test.Test)

====================================================================== FAIL: test (tests.mutually_exclusive_exons_novel.test.NovelJunction)

====================================================================== FAIL: test (tests.mutually_exclusive_exons_novel.test.NovelSpliceSite)

====================================================================== FAIL: test (tests.only_one_sample.test.StatOffTest)

====================================================================== FAIL: test (tests.only_one_sample.test.StatOnTest)

====================================================================== FAIL: test (tests.overlapped_gene.test.Test)

====================================================================== FAIL: test (tests.paired_stats.test.FilteredEventTest)

====================================================================== FAIL: test (tests.paired_stats.test.OneEventTest)

====================================================================== FAIL: test (tests.paired_stats.test.TwoEventTest)

====================================================================== FAIL: test (tests.prep_post.test.Test)

====================================================================== FAIL: test (tests.retained_intron_novel.test.NovelJunction)

====================================================================== FAIL: test (tests.retained_intron_novel.test.NovelSpliceSite)

====================================================================== FAIL: test (tests.skipped_exon_basic.test.Test)

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelJunction)

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelSpliceSite)

====================================================================== FAIL: test (tests.skipped_exon_novel.test.NovelSpliceSiteNotNovelJunction)

====================================================================== FAIL: test (tests.stranded.test.FirstStrandTest)

====================================================================== FAIL: test (tests.stranded.test.SecondStrandTest)

====================================================================== FAIL: test (tests.stranded.test.UnstrandedTest)

====================================================================== FAIL: test (tests.task_stat.test.Test)

====================================================================== FAIL: test (tests.variable_read_length.test.Length1Test)

====================================================================== FAIL: test (tests.variable_read_length.test.Length1VariableTest)

====================================================================== FAIL: test (tests.variable_read_length.test.Length2Test)

====================================================================== FAIL: test (tests.variable_read_length.test.Length2VariableTest)

====================================================================== FAIL: test (tests.variable_read_length.test.NoLengthTest)