Error when converting GFF3 to GTF2

[ale07alvarez]

reformat_transcripts --annotation_files Drosophila_melanogaster.BDGP6.28.100.sorted.gff3 --annotation_format GFF3 --sorted --output_format GTF2 Drosophila_melanogaster.BDGP6.28.100.sorted.gtf2
Traceback (most recent call last):
File "###/opt/anaconda3/envs/plastid/bin/reformat_transcripts", line 11, in
load_entry_point('plastid==0.4.7', 'console_scripts', 'reformat_transcripts')()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 488, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2861, in load_entry_point
return ep.load()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2461, in load
return self.resolve()
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/pkg_resources/init.py", line 2467, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/plastid/init.py", line 44, in
from plastid.genomics.genome_array import (BAMGenomeArray,
File "###/opt/anaconda3/envs/plastid/lib/python3.6/site-packages/plastid/genomics/genome_array.py", line 215, in
from plastid.genomics.map_factories import *
File "libchtslib.pxd", line 2530, in init plastid.genomics.map_factories (/anaconda/conda-bld/plastid_1494346258083/work/plastid-0.4.7/plastid/genomics/map_factories.c:26281)
ValueError: pysam.libchtslib.HTSFile has the wrong size, try recompiling. Expected 88, got 80

[AmmarDharani]

Hi @ale07alvarez,

I was experiencing the same error. The way I fixed it was switching my environment to Python 2.7 instead of Python 3.6. The error disappeared and I could use Plastid fine afterwards. If you're using Anaconda, make a new environment with Python v. 2.7: conda create --name py2 plastid python=2.7 and then once you activate the new environment conda activate py2, the error will go away.

[joshuagryphon]

Hi folks-
It's two years later. Is this still relevant?

[bribibel]

Thank you @AmmarDharani! I was having a problem trying to run metagene from a conda-downloaded version, getting (I think) similar errors and a Bio.Alphabet error, but I installed using your method and it seems to be running. Thank you!