Velvet error

[dicty]

Hi,

I tried to run sequence assembling against a reference genome with Velvet, but got error message as below.

[42.392250] Read 1 of length 32773, longer than limit 32767
[42.392259] You should modify ShortLength to int32_t in globals.h (around) line 84, recompile and re-run

How to resolve the problem? What's "modify ShortLength to int32)in in globals.h"?

Thanks a lot!

Dicty

[Thorondor]

http://www.ebi.ac.uk/~zerbino/velvet/

i think velvet thinks your "reference" is a read for assembly and therefore it's too long. If I am wrong there is a -long option for long reads.

If I am right:
velvet does NOT support assembling with a reference! for that you need the extension Columbus, read the Columbus manual. try again. ask again for help. ;-)

[dicty]

I just followed the Columbus manual, but got the error message. Yes, there is a -long option for long reads, but I still got the same error message.

[Thorondor]

vell ok. sry then.

I suggest to do what the error tells you. Go to

/bin/velvet/velvet_1.0.18/src/

open globals.h
and change the line:
typedef int32_t ShortLength;
to
typedef int64_t ShortLength;

compile velvet again, try again. the line is just below "#ifdef LONGSEQUENCES".
hope this helps.

[dicty]

Thorondor,

Thank you very much for your help. I just made the change following the error message. It's working now.

Again, really appreciate your suggestion.

Dicty

[maria.b]

Hi

I have quite the same problem and I don't understand why

[338.503721] Read 1 of length 32785, longer than limit 32767
[338.503727] You should modify recompile with the LONGSEQUENCES option (cf. manual)

I'm using velvet against on sequence of 33Mb, with 51,415,694 short reads of 101 bp. So I don't understand what is the "Read 1 of length 32785".

what is the "LONGSEQUENCES option"? Is that when we declare our library with -long option ?

Maria

[maria.b]

The answer is a title of the manual, well done Maria!

I'm tired sorry!

But I still do not understand why Velvet detect a read of 32785 bp. Does someone have an idea?

[chariko]

I am getting the same error:

velveth 21 21 -reference Reference.fna -shortPaired -sam 1D14.sam

[0.000001] Reading FastA file Reference.fna;
[1.264527] 90 sequences found
[1.264545] Done
[1.264555] Reading SAM file 1D14.sam
[12.113724] 3364950 reads found.
[12.113741] Done
[12.113745] Reference mapping counters
[12.113749] Name Read mappings
...
[12.114339] Reading read set file 21/Sequences;
[12.677591] 3365040 sequences found
[12.677667] Read 1 of length 32794, longer than limit 32767
[12.677674] You should modify recompile with the LONGSEQUENCES option (cf. manual)

I got my sam file by aligning paired end fastq file with bwa.

I made Thorondorś change and it did not work (although it was not exactly the same error).


Edited:

I did the make 'LONGSEQUENCES=Y' and it worked.