search

jtlovell / GENESPACE

Other
180 stars 24 forks source link

Combining and annotating bed files w/ OGs and tandem array info fails #136

Closed Jadziaa closed 7 months ago

Jadziaa commented 7 months ago

Dear GENESPACE team,

I am trying to replicate the plot from the GENESPACE tutorial using the test data ("human", "mouse", "platypus", "chicken", "sandLizard") on the Ubuntu 20.04.6 LTS cluster and I run into problems at the second step of the conduction GENESPACE run (Combining and annotating bed files w/ OGs and tandem array info).

I am using Orthofinder 2.5.5 and diamond 2.011. And The previous step calling init_genespace showed all the dependencies are valid:

Checking dependencies ... Found valid path to OrthoFinder v2.55: orthofinder Found valid path to DIAMOND2 v2.011: diamond Found valid MCScanX_h executable: /home2/jadzia/tools/MCScanX/MCScanX_h

Everything seems to working until I am getting following error:

  1. Combining and annotating bed files w/ OGs and tandem array info ... realloc(): invalid old sizerealloc(): invalid pointerrealloc(): invalid pointer realloc(): invalid pointer caught segfault

    caught segfault

    caught segfault

    caught segfault address 0x40, cause 'memory not mapped'

    caught segfault

    caught segfault

address 0x5583cbdd223c, cause 'memory not mapped'

caught segfault

caught segfault

caught segfault

caught segfault

caught segfault

caught segfault

caught segfault address 0x1b0, cause 'memory not mapped'

caught segfault address 0x6c, cause 'memory not mapped'

caught segfault

caught segfault address 0xcc, cause 'memory not mapped'

caught segfault address 0xfffffffa, cause 'memory not mapped'

caught segfault address 0x114, cause 'memory not mapped' Aborted (core dumped)

I would be grateful for any suggestions on how to fix this issue.

Thank you in advance.

jtlovell commented 7 months ago

I am not sure ... this looks like an issue with your machine's architecture, or maybe your R installation? Perhaps try on another machine/node?