segment:error in gene level segmentation

[snk9987]

I tried it with the ensemble annotation and I received the following error:

Executing the following command: iCount segment Homo_sapiens.GRCh38.93.gtf Homo_sapiens.GRCh38.93.seg.gtf GRCh38.p7.genome.fa.fai Input parameters for function 'get_segments' in iCount.genomes.segment annotation: Homo_sapiens.GRCh38.93.gtf segmentation: Homo_sapiens.GRCh38.93.seg.gtf fai: GRCh38.p7.genome.fa.fai report_progress: False Calculating intergenic intervals... Segmentation stored in Homo_sapiens.GRCh38.93.seg.gtf Making also gene level segmentation... [FileNotFoundError] 2 File "/home/icuser/iCount_src/iCount/cli.py", line 439, in main result_object = func(**args)

File "/home/icuser/iCount_src/iCount/genomes/segment.py", line 1037, in get_segments make_regions(segmentation, out_dir=os.path.dirname(segmentation))

File "/home/icuser/iCount_src/iCount/genomes/segment.py", line 357, in make_regions os.makedirs(out_dir, exist_ok=True)

File "/home/icuser/.icountenv/lib/python3.4/os.py", line 237, in makedirs mkdir(name, mode)

[JureZmrzlikar]

This was a known issue and it should been fixed if you use latest version. Please re-install the latest version of ICount, like described here.