Reapr perfectmap issue

Question

[fhsantanna]

Hi.

I am using Reapr in order to validate my assemblies. I have a paired-end Miseq library data from a bacterial genome.

After executing the perfectmap command ($reapr perfectmap bacter_reapr.fasta AO32_S1_L001_R1_001.fastq AO32_S1_L001_R2_001.fastq 400 perfect_bacter), I receive the following error:

Reading all chromosomes from bacter_reapr.fasta ... read 53 chromosomes.
Indexing 53 chromosomes ... sorting ... done.
Setting read length to 163
Using binmask 01000000
Reading solexa pair data from perfect_bacter.tmp.reads_1.fq ... terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr
[REAPR perfect_map] Error in system call:
/opt/Reapr_1.0.17/src/findknownsnps --genome=Lysobacter_reapr.fasta --fastq=perfect_bacter.tmp.reads_1.fq --fastq2=perfect_lysobacter.tmp.reads_2.fq --bins=perfect_bacter.tmp.bin --binmask=0100 --fragment=400 --variance=200 --chop=10

Any ideas?

[fhsantanna]

I found the problem. All reads must have the same size.

[prawat2009]

What do you mean all reads should have same size ? if an assembly has different sized reads, reapr will not map perfectly?