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Dear all,
I have tried to use igia to integrate data which were obtained by different sequencing platforms.
I think installation of igia was successfully completed because demo.sh was finished without any problems.
I typed the following command,
igia --tgs Isoseq.s.bam --tss TSS.tsv --tes TES.tsv --ngs illumina.s.bam -o igia_res
and then, I got the error below.
What do I have to improve?
Thanks in advance,
Jung
`Traceback (most recent call last):
File "/home/owner/miniconda2/envs/igia/bin/igia", line 10, in <module>
sys.exit(run())
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/skeleton.py", line 215, in run
main(sys.argv[1:])
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/skeleton.py", line 189, in main
chrom, start, end, ngs_obj_list, tgs_obj_list, ext_tss_list, ext_tes_list, ann, f_genome, paraclu_path)
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 1239, in identify_element
gene.identify_element(tmp_ext_tss_site_list, tmp_ext_tes_site_list, paraclu_path)
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 499, in identify_element
self.identify_intron()
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 389, in identify_intron
intron_set_ngs = set(NgsElementDiscover.identify_intron(self.ival, self.ngs_bam_list))
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 953, in identify_intron
intron_list = ngs_junction_graph.identify_intron(ngs_bams)
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 1179, in identify_intron
self._build(bam_list)
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/element.py", line 1158, in _build
lambda x: self._is_junction_read(x), bam.fetch_reads_in_ival(self.ival)))
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/utils.py", line 158, in fetch_reads_in_ival
return list(clean_ival_read_iter)
File "/home/owner/miniconda2/envs/igia/lib/python3.6/site-packages/igia/utils.py", line 150, in <lambda>
lambda x: x.reference_start >= start and x.reference_end <= end, ival_read_iter)
TypeError: '<=' not supported between instances of 'NoneType' and 'int'`
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