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h5py TypeError: No conversion path for dtype: dtype('<U18') #57

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huipan1973 opened this issue Jul 20, 2023 · 0 comments
Open

h5py TypeError: No conversion path for dtype: dtype('<U18') #57

huipan1973 opened this issue Jul 20, 2023 · 0 comments

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@huipan1973
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RiboCode -a RiboCode_annot -c metaplots_pre_config.txt -l no -g -o RiboCode_ORFs_result

Loading transcripts.pickle ...
Reading bam file: /n/jobspace/bbcore/schaffer_rpf_abby_min6/two_batches/rpf/alignments_transcriptome/20210125_Index_3_JS8600_S11_R1_001_Aligned.toTranscriptome.out.bam......
Traceback (most recent call last):
File "/home/panh/miniconda3/envs/ribocode/bin/RiboCode", line 10, in
sys.exit(main())
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/RiboCode/RiboCode.py", line 40, in main
tpsites_sum, total_psites_number = process_bam.psites_count(configIn.configList,transcript_dict,thread_num=1)
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/RiboCode/process_bam.py", line 118, in psites_count
tpsites,psites_number = read_bam(configData)
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/RiboCode/process_bam.py", line 80, in read_bam
write_psites(tpsites,psites_number, name + "_psites.hd5")
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/RiboCode/process_bam.py", line 21, in write_psites
fout.create_dataset("transcript_ids",data=list(tpsites.keys()),dtype=ds)
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/h5py/_hl/group.py", line 136, in create_dataset
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
File "/home/panh/miniconda3/envs/ribocode/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 170, in make_new_dset
dset_id.write(h5s.ALL, h5s.ALL, data)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "h5py/h5d.pyx", line 212, in h5py.h5d.DatasetID.write
File "h5py/h5t.pyx", line 1654, in h5py.h5t.py_create
File "h5py/h5t.pyx", line 1715, in h5py.h5t.py_create
TypeError: No conversion path for dtype: dtype('<U18')

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