Picard SamToFastq strange behavious

[reema]

Dear all,

I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-

java -jar SamToFastq.jar INPUT=input.bam FASTQ=input_1.fastq SECOND_END_FASTQ=input_2.fastq VALIDATION_STRINGENCY=LENIENT

The command runs without error and generate two file. Now the problem is input_1.fastq has all the reads where as input_2.fastq is empty(o byte file). I have no idea why it's happening. I tried following option but no luck,
1) Sorted bam -> SamToFastq
2) BAM to SAM -> SamToFastq

Any suggestion would be very helpful.

Thanks,
Reema SIngh

[TiborNagy]

Maybe you BAM file is not a paired end sample. Check it manually.

[reema]

Maybe you BAM file is not a paired end sample. Check it manually.

Thanks TiborNagy,

You are right,my file is not paired..