Opera Scaffolding Error: Reads In The Wrong Orientation

Question

[HG]

Hi everyone I am using Opera for Scaffolding with mapping tool bwa . I am getting an error : Please help me out

I am using like this

perl preprocess_reads.pl contigsH10.fasta ResetH10_S1_L001_R1_001.fastq ResetH10_S1_L001_R2_001.fastq lib_1.map bwa
------------------------------------------------
[main] Version: 0.6.1-r104
[main] CMD: bwa samse -n 1 contigsH10.fasta read.sai -
[main] Real time: 14.802 sec; CPU: 14.149 sec
[Fri Sep  6 12:45:56 2013]    Preprocessing done!

./opera contigsH10.fasta lib_1.map outH10

Step 1: Setting parameters ...
Time Taken: 0.000135 seconds
Step 2: Reading contig file ...
Time Taken: 0.012631 seconds
Step 3: Reading mapping file ...
The orientation of reads is not "in", "out", neither "forward", Opera could not handle such orientation. Please check the mapping files. Please feel free to contact [e-mail] for further support. 
ERROR: Converting mapping file error!

Answer 1

[Pierre Lindenbaum]

Opera is a "Optimal Paired-End Read Assembler" but you used the single-end mapper of bwa (samse)

[HG]

I am using like this in command line

$ perl bin/preprocess_reads.pl test_dataset/contigs_H10.fasta test_dataset/ResetH10_S1_L001_R1_001.fastq.gz test_dataset/ResetH10_S1_L001_R2_001.fastq.gz test_dataset/lib_1.bam bwa

Next :

$ bin/opera test_dataset/contigs_H10.fasta test_dataset/lib_1.bam,test_dataset/lib_2.bam test_dataset/results2

Could you please have a look the command ?