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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?

assembly software error next-gen
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updated by GenoMax GenoMax • written by vramirezc • vramirezc

1 answer

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. 

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written by vramirezc • vramirezc

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