baoxingsong/AnchorWave

example data core dumped "{EXE}_sse4.1""$@"

HozumiLv opened this issue · 6 comments

HozumiLv commented

Hi, Dr Song,

Thanks for your wonderful tool. I meet an error when run the example(guideline zea & sorghum).

wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/fasta/zea_mays/dna/Zea_mays.AGPv4.dna.toplevel.fa.gz
wget ftp://ftp.ensemblgenomes.org/pub/plants/release-34/gff3/zea_mays/Zea_mays.AGPv4.34.gff3.gz
wget http://ftp.ensemblgenomes.org/pub/plants/release-54/fasta/sorghum_bicolor/dna/Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa.gz

gunzip *.gz

anchorwave gff2seq -r Zea_mays.AGPv4.dna.toplevel.fa -i Zea_mays.AGPv4.34.gff3 -o cds.fa
minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa cds.fa > cds.sam
minimap2 -x splice -t 10 -k 12 -a -p 0.4 -N 20 Zea_mays.AGPv4.dna.toplevel.fa cds.fa > ref.sam

anchorwave proali -i Zea_mays.AGPv4.34.gff3 -as cds.fa -r Zea_mays.AGPv4.dna.toplevel.fa -a cds.sam -ar ref.sam -s Sorghum_bicolor.Sorghum_bicolor_NCBIv3.dna.toplevel.fa -n align.anchors -R 1 -Q 2 -t 1 -o alignment.maf -f alignment.f.maf

Then I got a "core dumped" error when running proali. Here is the message:
line 22: 3415 Segmentation fault core dumped "{EXE}_sse4.1""$@"

Do you have any idea about this error? Thanks!
Lv

baoxingsong commented

Hi, Lv

I could not repeat your error message.

image

May I ask how did you install AnchorWave? Via source code compiling or conda? Which version are you using?

Are your using cluster? Are you using different CPUs to install AnchorWave and run AnchorWave, please? For example, install it on an X86 CPU but run it on an ARM CPU?

If you would like to run AnchorWave on an ARM CPU, please refer to this document.
https://github.com/baoxingsong/AnchorWave/blob/master/installation.md

HozumiLv commented

Hi, Dr Song,

I used conda to install AnchorWave，I use AnchorWave version 1.2.1.
I only used x86 CPU to install and run AnchorWave.
image

Best,
Lv

baoxingsong commented

Could you run cat /proc/cpuinfo, free -h, anchorwave, ls -ls and share the screenshot, please?

HozumiLv commented

  1. cat /proc/cpuinfo
    cpuinfo.txt

  2. free -h
    image

  3. anchorwave
    image

  4. ls -ls
    image

Thanks!

baoxingsong commented

I did not find any potential problem with your screenshot.

Since I could not repeat your error, this problem might not be solved quickly.
If you give me access to your computer, that would help. songbaoxing168@163.com

HozumiLv commented

Ok, thank you very much!