Segmentation fault on hg38

[millerh1]

Hello -- I am having trouble using G4Hunter on the hg38 FASTA from UCSC.

It starts fine, but after about ~10 minutes, it crashes with a Segmentation fault:

~$ python2 G4Hunter.py -i ~/.rlpipes_genomes/hg38/hg38.fa -o "../" -w 25 -s "1.2"
true Results_hg38

         Re-evaluation of G-quadruplex propensity with G4Hunter

#####################################
#    New Results directory Created  #
#####################################


 Input file: hg38
Segmentation fault (core dumped)

[AnimaTardeb]

https://stackoverflow.com/questions/19641597/what-is-segmentation-fault-core-dumped A.B

…

On May 1, 2022, at 6:17 PM, Henry Miller ***@***.***> wrote: Segmentation fault (core dumped

[millerh1]

I am not running out of RAM if that is what you are implying. I'm on a machine with 256GB and running G4Hunter doesn't add more than 10GB from baseline.

I also do not experience Segmentation faults with any other python programs.

[AnimaTardeb]

Hello,

im not implying anything. it't the first time i see the segmentation fault on python i usually see it on c++
i did run the hg19 not the problem ...

1: -s "1.2"=> why " "

2: have you tied to run first the test? do you have segmentation fealt with a test file

3: why the "" in -o "../"?
4: why are you using python2 ? i code it on 2.7

[millerh1]

Thank you for looking into this! Here are my responses to your questions:

1. Just a personal preference -- I will remove them.
2. I just ran it and it worked fine:

~$ python2 G4Hunter.py -i Mitochondria_NC_012920_1.fasta -o ../ -w 25 -s 1.2
true Results_Mitochondria_NC_012920_1

         Re-evaluation of G-quadruplex propensity with G4Hunter

#####################################
#    New Results directory Created  #
#####################################


 Input file: Mitochondria_NC_012920_1

 Results files and Score Figure are created in:
../ / Results_Mitochondria_NC_012920_1 /

3. Same as (1)
4. I am using python 2.7.18 which is aliased as python2 on my machine.

[AnimaTardeb]

it better if you create a folder inside your ../ and send the results there
could you please run the hg38 without the "" ?
if not try to do just 1 chromosome and see because 10 min still on the 1 chr

try another genome from your collection
I know a lot of ppl + me have run the hg19 and succeeded
beside this i really don't see where the problem cam from !!

[millerh1]

It worked when applied to just Chr1 from UCSC hg38:

~$ python2 G4Hunter.py -i chr1.fa -o ../ -w 25 -s 1.2                      
########################################################################
#                            Results directory Created                 #
########################################################################


 Input file: chr1

 Results files and Score Figure are created in:
../ / Results_chr1 /

Unsure of why it would fail on the whole genome then.

[millerh1]

After working with this for a bit, I am still getting intermittent segfaults -- still unsure of why though.

[AnimaTardeb]

sorry for the delay.
I might have an idea but I really don't have a time to go back to my scripts.it been 6 years
did you try each chromosome separately? I know it's long sorry for that