SNAP prediction erro

[unavailable-2374]

zff2gff3.pl prediction.snap.txt | gffread -E --force-exons -O -F -o - .....

Segmentation fault (core dumped)

prediction.snap.txt: """

M1_hap1_chr01 Einit 3257 3373 - -6.432 0 0 2 M1_hap1_chr01-snap.1 Exon 2739 3026 - 8.987 0 0 1 M1_hap1_chr01-snap.1 Exon 2311 2619 - 5.596 0 0 0 M1_hap1_chr01-snap.1 Eterm 722 799 - -6.641 0 0 2 M1_hap1_chr01-snap.1 Einit 8970 9222 - 25.445 0 1 0 M1_hap1_chr01-snap.2 Exon 7446 7455 - 13.580 2 2 2 M1_hap1_chr01-snap.2 Eterm 7201 7297 - 15.205 1 0 0 M1_hap1_chr01-snap.2 Einit 14092 14147 - 2.203 0 2 1 M1_hap1_chr01-snap.3 Exon 13713 13997 - -30.601 1 2 2 M1_hap1_chr01-snap.3 Exon 13197 13310 - 3.035 1 2 2 M1_hap1_chr01-snap.3 Exon 12888 13095 - 1.833 1 0 1 M1_hap1_chr01-snap.3 Eterm 9238 9261 - 6.719 0 0 0 M1_hap1_chr01-snap.3 Einit 14214 14744 + -14.381 0 0 2 M1_hap1_chr01-snap.4 Exon 15083 15470 + -3.806 0 1 1 M1_hap1_chr01-snap.4 Eterm 15654 15817 + 9.817 2 0 1 M1_hap1_chr01-snap.4 Esngl 15872 16885 + 21.195 0 0 1 M1_hap1_chr01-snap.5 Einit 16892 17065 + 0.466 0 0 1 M1_hap1_chr01-snap.6 Exon 20490 20596 + 18.166 0 2 2 M1_hap1_chr01-snap.6 Exon 20697 20840 + 6.386 1 2 0 M1_hap1_chr01-snap.6 Eterm 22763 22811 + 18.577 1 0 2 M1_hap1_chr01-snap.6 """

after i try to run the zff2gff3.pl

"""

gff-version 3

region M1_hap1_chr01

M1_hap1_chr01 snap CDS 3257 3373 . - Name=M1_hap1_chr01-snap.1 M1_hap1_chr01 snap CDS 2739 3026 . - Name=M1_hap1_chr01-snap.1 M1_hap1_chr01 snap CDS 2311 2619 . - Name=M1_hap1_chr01-snap.1 M1_hap1_chr01 snap CDS 722 799 . - Name=M1_hap1_chr01-snap.1 M1_hap1_chr01 snap CDS 8970 9222 . - Name=M1_hap1_chr01-snap.2 M1_hap1_chr01 snap CDS 7446 7455 . - Name=M1_hap1_chr01-snap.2 M1_hap1_chr01 snap CDS 7201 7297 . - Name=M1_hap1_chr01-snap.2 M1_hap1_chr01 snap CDS 14092 14147 . - Name=M1_hap1_chr01-snap.3 M1_hap1_chr01 snap CDS 13713 13997 . - Name=M1_hap1_chr01-snap.3 M1_hap1_chr01 snap CDS 13197 13310 . - Name=M1_hap1_chr01-snap.3 M1_hap1_chr01 snap CDS 12888 13095 . - Name=M1_hap1_chr01-snap.3 M1_hap1_chr01 snap CDS 9238 9261 . - Name=M1_hap1_chr01-snap.3 M1_hap1_chr01 snap CDS 14214 14744 . + Name=M1_hap1_chr01-snap.4 M1_hap1_chr01 snap CDS 15083 15470 . + Name=M1_hap1_chr01-snap.4 M1_hap1_chr01 snap CDS 15654 15817 . + Name=M1_hap1_chr01-snap.4 M1_hap1_chr01 snap CDS 15872 16885 . + Name=M1_hap1_chr01-snap.5 M1_hap1_chr01 snap CDS 16892 17065 . + Name=M1_hap1_chr01-snap.6 M1_hap1_chr01 snap CDS 20490 20596 . + Name=M1_hap1_chr01-snap.6 M1_hap1_chr01 snap CDS 20697 20840 . + Name=M1_hap1_chr01-snap.6 M1_hap1_chr01 snap CDS 22763 22811 . + Name=M1_hap1_chr01-snap.6 """

and then I use it to run the gffread ,erro happend

Could you help me to solve it , thanks!

zhou

[andreaminio]

Hi Zhou,

I never had runtime errors with gffread, it may be that zff2gff3.pl is producing some weird result. I cannot be sure 100% as the tabbing of the output file is gone, but a correct gff3 should have 9 columns and it seems your output is missing the phase column for some reaso. This may be the origin of the issue, however I'm not sure if in such a case gffread would throw a core dump or a different kind of error.

Andrea

[unavailable-2374]

Hi Andrea

thank you for your reply!!!

It has confused me for too long,but as you see the zff2gff3.pl just print out 8 columns :

could you share your zff2gff3.pl to me , or tell me how to fix this script , truly thanks!

zhou

[zhouyflab]

I try to fix the script by add a columns like this

but it still not work

the cmd told me

""" gffread -E --force-exons -O -F -o - .. loaded 0 genomic features from stdin """

I am so curious, and my project really need your pipeline to annotation genome , could you help me

my sincerely thanks !

zhou

[andreaminio]

Hi Yongfeng,

I see my zff2gff3.pl script is probably older and different exactly in that line. I added a copy of it in the script folder.

Now, to gffread issue, it seems that the file stream in input is reaching the script but is not able to parse it correctly and read any feature form it. From what I see, however, the structure of the input is the one of a correct GFF3, so it looks pretty weird. It may be a hidden issue, did you check the new line symbols (unix ones, not windows) and the separators (only tabs, no multiple spaces)? These issues may be difficult to spot, and in the picture or text online I cannot verify it.

Andrea

[zhouyflab]

Thank you very much! I will forward this to my student.

Cheers, Yongfeng

--

Prof. Yongfeng Zhou Professor of Horticulture at AGIS, CAAS Population Genomics and Genomic Breeding of Grapevine Cell/Wechat: 13924607807, twitter: @yongfeng_zhou Email: @.**@. The Agricultural Genomics Institute at Shenzhen, The Chinese Academy of Agricultural Sciences

From: Andrea Minio @.> Date: 2022-05-31 23:49:59 To: andreaminio/AnnotationPipeline-EVM_based-DClab @.> Cc: zhouyflab @.>,Comment @.> Subject: Re: [andreaminio/AnnotationPipeline-EVM_based-DClab] SNAP prediction erro (Issue #5)

Hi Yongfeng, I see my zff2gff3.pl script is probably older and different exactly in that line. I added a copy of it in the script folder. Now, to gffread issue, it seems that the file stream in input is reaching the script but is not able to parse it correctly and read any feature form it. From what I see, however, the structure of the input is the one of a correct GFF3, so it looks pretty weird. It may be a hidden issue, did you check the new line symbols (unix ones, not windows) and the separators (only tabs, no multiple spaces)? These issues may be difficult to spot, and in the picture or text online I cannot verify it. Andrea — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>