Error Creating Custom reference for genome

ivanferrreira commented 3 years ago

Hi Jiekai Lab - thank you for developing such great resouce!

I keep on having an issue to create custom genomes for scRNA analysis. Even when I run the example data with: scTE_build -te ./Data/TE.bed -gene ./Data/Gene.gtf -o test.idx

I get the error: "Counting genome other not supported"

Could you please help me? I've ruled out installation issues as I don't have any other problems in reproducing the other parts of your pipeline (e.g., with scATAC or built in genomes)

Thank you

Ivan Ferreira Sauka-Spengler Lab

jphe commented 3 years ago

Hi Ivan,

We have update the scTE and should be fixed now, can you try again with the newest version.

Jphe

ivanferrreira commented 3 years ago

Hi Jphe, thank you for getting back to me so quickly, very appreciated

Do you mind sending me instructions on how to update to the newest version?

Ivan

From: jphe @.> Sent: Thursday, May 27, 2021 4:09 AM To: JiekaiLab/scTE @.> Cc: Ivan Candido Ferreira @.>; Author @.> Subject: Re: [JiekaiLab/scTE] Error Creating Custom reference for genome (#15)

Hi Ivan,

We have update the scTE and should be fixed now, can you try again with the newest version.

Jphe

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/JiekaiLab/scTE/issues/15#issuecomment-849283958, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AQEDISWQUF2DX4H7P75EG33TPWZYDANCNFSM45STXHVA.

jphe commented 3 years ago

Just remove the old one, and then reinstall it.

git clone https://github.com/JiekaiLab/scTE.git
cd scTE
python setup.py install

ivanferrreira commented 3 years ago

Thank you

I just finished removing the old one and reinstalling - it seems something is still a bit off with the scTE_build function, but not the others

I am now gettting the following error message now with the test data:

INFO : Building the scTE genome annotation index... 2021-05-27 09:45:52

/gpfs3/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE_build:110: DeprecationWarning: 'U' mode is deprecated

o = open(tefile,'rU')

Traceback (most recent call last):

File "/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/bin/scTE_build", line 4, in

__import__('pkg_resources').run_script('scTE==1.0', 'scTE_build')

File "/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/pkg_resources/init.py", line 666, in run_script

self.require(requires)[0].run_script(script_name, ns)

File "/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/pkg_resources/init.py", line 1462, in run_script

exec(code, namespace, namespace)

File "/gpfs3/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE_build", line 468, in

main()

File "/gpfs3/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE_build", line 461, in main

genomeIndex(args.genome,args.mode,tefile,genefile, args.out,'No path','No path')

File "/gpfs3/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/EGG-INFO/scripts/scTE_build", line 127, in genomeIndex

gls.load_list(clean)

File "/well/combat/users/akt326/devel/ivybridge/python3-venv-ivybridge-3.8.2/lib/python3.8/site-packages/scTE-1.0-py3.8.egg/scTE/miniglbase/genelist.py", line 1472, in load_list

list_to_load[0]

IndexError: list index out of range

jphe commented 3 years ago

We can not repeat your error, can you check the bed (6 columns) and gtf file format are correct?

JiekaiLab / scTE

Error Creating Custom reference for genome #15