build mode issue

[khksw0403]

• spladder version: 3.0.3
• Python version: 3.9.12
• Operating System: Ubuntu 22.04.1 LTS

Description

popup with error msg:

File "/root/anaconda3/lib/python3.9/site-packages/spladder-3.0.3-py3.9.egg/spladder/editgraph.py", line 611, in insert_intron_edges
print('%s\talternative_53_prime1\t%c\t%i\t%i\t%i\n' % (genes[i].chr, genes[i].strand, genes[i].splicegraph,vertices[1, idx1_],
NameError: name 'vertices' is not defined

What I Did

spladder build
-b STAR-2pass bam files
-o output path
-a anootation gtf file
-v
-d
--filter-overlap-genes
--filter-overlap-exons
--filter-overlap-transcripts
-l MPM152
--output-gff3
--output-bed
-c 3
--extract-ase
--parallel 8
--validate-sg --validate-sg-count 10
--quantify-graph
--use-anno-support
--psi-min-reads 10
--qmode collect

file:///home/kkang/Pictures/Screenshots/spladder.png

[raerose01]

Hi, I am also getting the same error (same version of Spladder, running on Linux 3.10.0-957.21.3.el7.x86_64). I was curious if there was any workaround. Thanks!

[akahles]

Dear @khksw0403 & @raerose01 ,
Thank you for reporting the issue. This seems to be a bug when SplAdder is run with -d flag for debug output in certain scenarios. A quick workaround is to remove the -d flag from your commands. I have already pushed a fix, which will become available shortly with the next version.
Best,
Andre

[raerose01]

Thanks @akahles , removing the debug flag worked for me.

[khksw0403]

Thanks @raerose01 & @akahles.
work for me :)