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adamewing / tldr

Identify and annotate TE-mediated insertions in long-read sequence data
MIT License
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python exception running tldr test #11

Open blurdeblur opened 3 years ago

blurdeblur commented 3 years ago

I ran the test and got this error:

2021-02-03 15:17:21,431 te-ont started with command: /root/anaconda3/envs/R4/bin/tldr -b test.bam -e teref.human.fa -r ref.fa --color_consensus 2021-02-03 15:17:21,431 output basename: test 2021-02-03 15:17:21,658 writing clusters to test/chrTEST.pickle 2021-02-03 15:17:21,789 loaded 14 clusters from test/chrTEST.pickle multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/root/anaconda3/envs/R4/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, **kwds)) File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/tldr-0.1-py3.7.egg/EGG-INFO/scripts/tldr", line 1198, in process_cluster File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/tldr-0.1-py3.7.egg/EGG-INFO/scripts/tldr", line 983, in minimap2_profile File "pysam/libcalignmentfile.pyx", line 742, in pysam.libcalignmentfile.AlignmentFile.cinit File "pysam/libcalignmentfile.pyx", line 947, in pysam.libcalignmentfile.AlignmentFile._open ValueError: file does not contain alignment data """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/root/anaconda3/envs/R4/bin/tldr", line 4, in import('pkg_resources').run_script('tldr==0.1', 'tldr') File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/pkg_resources/init.py", line 650, in run_script self.require(requires)[0].run_script(script_name, ns) File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/pkg_resources/init.py", line 1453, in run_script exec(script_code, namespace, namespace) File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/tldr-0.1-py3.7.egg/EGG-INFO/scripts/tldr", line 1811, in File "/root/anaconda3/envs/R4/lib/python3.7/site-packages/tldr-0.1-py3.7.egg/EGG-INFO/scripts/tldr", line 1648, in main File "/root/anaconda3/envs/R4/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value ValueError: file does not contain alignment data

I wonder if you can tell me what I did wrong? Thank you,

adamewing commented 3 years ago

Sorry I missed this one, it's been ages but let me know if you've resolved this or not. My guess is a dependency might be missing (minimap2 maybe?)