search

barricklab / breseq

breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA resequencing data. It is intended for haploid microbial genomes (<20 Mb). breseq is a command line tool implemented in C++ and R.
http://barricklab.org/breseq
GNU General Public License v2.0
137 stars 21 forks source link

gdtools problem #332

Closed ihara920 closed 1 year ago

ihara920 commented 1 year ago

I don't understand the following warning. I use breseq v 0.37.1 comand: $ gdtools COMPARE -o test.html -r /home/DATA/Ref/pombe_ASM294v2.gbk WT.gd 93-A.gd

In this case, I used the small genome eukaryote Sc.pombe and work well in the breseq analysis. But it failed to compare in gdtools.

Begin ANNOTATE/COMPARE 

Reading input reference sequence files
    /home/DATA/Ref/pombe_ASM294v2.gbk

----------------------------------> WARNING <----------------------------------- Ignoring repeat feature that has complex/multiple locations. Name: Positions: start = 5565247 end = 5565349 strand -1 start = 5565067 end = 5565187 strand -1 start = 5564531 end = 5564853 strand -1

Reading input GD file: WT.gd

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Could not open file for reading: WT.gd FILE: genome_diff.cpp LINE: 59 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 8 stack frames. gdtools(+0x352a9) [0x5564627ba2a9] gdtools(+0xc09d3) [0x5564628459d3] gdtools(+0xc1f48) [0x556462846f48] gdtools(+0x7973a) [0x5564627fe73a] gdtools(+0x7b119) [0x556462800119] gdtools(+0x28dc4) [0x5564627addc4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3) [0x7f5bb67be083] gdtools(+0x32b69) [0x5564627b7b69] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

jeffreybarrick commented 1 year ago

The warning is related to your reference sequence being from a eukaryote. It won't affect things, but it is telling you that a repeat feature has multiple locations (maybe it's spliced together), so breseq won't be able to use it to predict a transposon insertion.

Again, this error, like the other ones, seems to be that the file WT.gd does not exist in your current working directory and can't be opened.

ihara920 commented 1 year ago

Thank you for your rapid reply. These (#331 and #332) are NOT your issue, but my issue about the symbolic link. So, I have checked my script, and gdtools work well now. Thank you again!

2022年11月10日(木) 5:39 Jeffrey Barrick @.***>:

The warning is related to your reference sequence being from a eukaryote. It won't affect things, but it is telling you that a repeat feature has multiple locations (maybe it's spliced together), so breseq won't be able to use it to predict a transposon insertion.

Again, this error, like the other ones, seems to be that the file WT.gd does not exist in your current working directory and can't be opened.

— Reply to this email directly, view it on GitHub https://github.com/barricklab/breseq/issues/332#issuecomment-1309348473, or unsubscribe https://github.com/notifications/unsubscribe-auth/AH6CMEHUS236V22KXJ2FRV3WHQDWVANCNFSM6AAAAAAR3HX6AA . You are receiving this because you authored the thread.Message ID: @.***>