Velvet Columbus (No roadmap)

esperando370 · 04-26-2020, 07:03 PM

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 · 04-28-2020, 10:41 AM

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.*

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04-26-2020, 07:03 PM	#1
esperando370 Junior Member Location: California Join Date: Apr 2020 Posts: 2	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?

04-28-2020, 10:41 AM	#2
esperando370 Junior Member Location: California Join Date: Apr 2020 Posts: 2	Solved! The problem was solvedjust 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.