SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Velvet Columbus unexpected results Y.G Bioinformatics 1 12-04-2018 02:53 AM
velvet columbus reference errors sfh838t De novo discovery 3 05-12-2014 04:54 AM
Francisco says Hi from Columbus, OH fpadilla Introductions 0 09-24-2012 04:11 PM
Columbus, Velvet color space SOLiD support pepperoni Bioinformatics 3 06-19-2012 04:18 AM
Reference sequence about Columbus for Velvet xxb0316 Bioinformatics 1 06-01-2011 05:10 AM

Reply
 
Thread Tools
Old 04-26-2020, 06:03 PM   #1
esperando370
Junior Member
 
Location: California

Join Date: Apr 2020
Posts: 2
Question Velvet Columbus (No roadmap)

Hi, I have been running velveth and velvetg for mapping on a reference file (Columbus extension) but I am getting the following error:

First I ran velveth, using the following script:
./velveth directory 21 -reference Concatenated.fasta -shortPaired -sam Bowtie2_sorted.sam

And the directory result was:

total 249760
drwxr-xr-x 2 vramirezc ucb 4096 Apr 24 11:26 ./
drwxr-xr-x 122 vramirezc ucb 12288 Apr 24 11:26 ../
-rw-r--r-- 1 vramirezc ucb 1158 Apr 24 11:53 Log
-rw-r--r-- 1 vramirezc ucb 255727679 Apr 24 11:26 Sequences

Later, I ran velvetg using:
./velvetg directory -ins_length 400 -exp_cov 10 -min_contig_lgth 100 -unused_reads yes

And then I just obtained an O file (the error file was empty) saying:
[0.000001] No Roadmap file to build upon! Please run velveth (see manual)
[0.000000] No Roadmap file to build upon! Please run velveth (see manual)
[0.000000] No Roadmap file to build upon! Please run velveth (see manual)
[0.000000] No Roadmap file to build upon! Please run velveth (see manual)

Clearly there is no roadmap in the directory file, but I do not know why. Could you please help me?
esperando370 is offline   Reply With Quote
Old 04-28-2020, 09:41 AM   #2
esperando370
Junior Member
 
Location: California

Join Date: Apr 2020
Posts: 2
Default Solved!

The problem was solved*just by recompiling the program using make 'LONGSEQUENCES=Y' (for some reason using make 'LONGSEQUENCES=1' did not work). It seems like the reference file was too long.*
esperando370 is offline   Reply With Quote
Reply

Tags
mapping reads, scaffolding, velvet, velvet paired-end, velveth

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO