ValueError: invalid literal for int() with base 10: '653057_RaGOO'

[neel404]

Hi Malonge.

I am getting the below error when I use float values for the flag -i. If I use an integer value, the job runs fine. Could you please give me your comments on this?

Loading ragoon/python3/1.11
Loading requirement: python3 minimap2/gcc-9.2.0/2.17
Traceback (most recent call last):
File "/cm/shared/apps/ragoo/python3/1.11/bin/filter_gap_SVs.py", line 4, in
import('pkg_resources').run_script('RaGOO==1.1', 'filter_gap_SVs.py')
File "/cm/local/apps/python3/lib/python3.7/site-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/cm/local/apps/python3/lib/python3.7/site-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
File "/cm/shared/apps/ragoo/python3/1.11/lib/python3.7/site-packages/RaGOO-1.1-py3.7.egg/EGG-INFO/scripts/filter_gap_SVs.py", line 125, in
File "/cm/shared/apps/ragoo/python3/1.11/lib/python3.7/site-packages/RaGOO-1.1-py3.7.egg/EGG-INFO/scripts/filter_gap_SVs.py", line 121, in main
File "/cm/shared/apps/ragoo/python3/1.11/lib/python3.7/site-packages/RaGOO-1.1-py3.7.egg/EGG-INFO/scripts/filter_gap_SVs.py", line 59, in make_svs_bed
File "/cm/shared/apps/ragoo/python3/1.11/lib/python3.7/site-packages/RaGOO-1.1-py3.7.egg/EGG-INFO/scripts/filter_gap_SVs.py", line 42, in get_query_bed_coords
ValueError: invalid literal for int() with base 10: '653057_RaGOO'
Traceback (most recent call last):
File "/cm/shared/apps/ragoo/python3/1.11/bin/ragoo.py", line 4, in
import('pkg_resources').run_script('RaGOO==1.1', 'ragoo.py')
File "/cm/local/apps/python3/lib/python3.7/site-packages/pkg_resources/init.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/cm/local/apps/python3/lib/python3.7/site-packages/pkg_resources/init.py", line 1470, in run_script
exec(script_code, namespace, namespace)
@
"stderr_file" 25L, 2284C

[malonge]

Hi there,

Could you share your command?

Also, if you are not too invested yet, I recommend you switch to using the new and improved version of RaGOO which is called RagTag:

https://github.com/malonge/RagTag

It's the same idea as RaGOO though a little more accurate and with a lot of nice new features. Regardless, I am happy to take a look into this RaGOO issue.

Thanks,
Mike

[neel404]

Hi Mike,

It was a misunderstanding. I am getting the mentioned error in both cases. It doesn't matter what value I use with the flag -i. Sorry for the inconvenience.

Following is the command I used ragoo.py Iaq6.scaffolds.fa NSP306_trifida_chr_v3.fa -b -t 40 -g 100 -s -i 0.2 -C

Also, Please guide me on how to use the same command with the new RagTag

Thanks in Advance.

Regards,
Jithin

[malonge]

Hi there,

with ragtag, you would do something like this:

ragtag.py correct -t 40 NSP306_trifida_chr_v3.fa Iaq6.scaffolds.fa
ragtag.py scaffold -t 40 -i 0.2 NSP306_trifida_chr_v3.fa ragtag_output/Iaq6.scaffolds.corrected.fasta

I notice you use the "-s" option, and structural variant calling is no longer supported in RagTag. I suggest you use paftools directly for that.

In fact, it is the SV calling here that is causing this error. It looks like you are using an older version. If you would like to continue using RaGOO for SV calling, I suggest installing the latest code since I have recently fixed some bugs in this exact script.

Thanks,
Mike

[malonge]

Please reopen the issue if anything comes up. Thanks