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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Error in Sliding_windows_3 #32

Closed jordangumm closed 6 years ago

jordangumm commented 6 years ago

I've tried multiple different parameter choices and rebuild my conda environment a few times, but I can't seem to fix an issue with the Sliding_windows_3 script. It doesn't matter if it's in virome (decontamination) mode or not, whether or not I set '--no_c', or if I set 'diamond', etc.

Error: Error in `/VirSorter/Scripts/Sliding_windows_3': realloc(): invalid pointer: 0x00007fffb8a3d110

I'm currently still investigating this issue, but any help would be highly appreciated. Perhaps this is an error that has been seen before? I noticed that the diamond version may have been a problem in another issue, but that resulted in a different error message.

simroux commented 6 years ago

Hi,

It looks like the issue for which the option "--no_c" had been implemented. This option should not call Sliding_windows_3, so I'm surprised you get an error referring to this script even when running VirSorter with "--no_c". Could you share the whole log_out file ? And, when using "--no_c", do you get the message at start-up "This is a 'no_c' run, so the C program in Step_3 will not be used and instead everything will be done in perl" as expected ?

jordangumm commented 6 years ago

I wasn't getting the "--no_c" message! Actually, I was getting:

Unknown option: no_c

Come to find out the version I was using was installed just before your June commit that added this option. Thanks for the help in figuring this out.