Unrecognized option: I picard.jar

Question

I am trying to convert a BMA file into FASTQ format, using picard.jar. This is my command:

java -jar /opt/picard-tools/picard.jar SamToFastq \ I=chr2chr3.bam \ FASTQ=chr2chr3.f1.fastq \ SECOND_END_FASTQ=chr2chr3.f2.fastq

However I got this error message:

ERROR: Unrecognized option: I

I am totally confused, Any thoughts?

Answer 1

remove the backslashes

java -jar /opt/picard-tools/picard.jar SamToFastq  I=chr2chr3.bam  FASTQ=chr2chr3.f1.fastq  SECOND_END_FASTQ=chr2chr3.f2.fastq

note:

• you can compress the fastqs, ignore the small errors in the BAM

  java -jar /opt/picard-tools/picard.jar SamToFastq I=chr2chr3.bam FASTQ=chr2chr3.f1.fastq.gz SECOND_END_FASTQ=chr2chr3.f2.fastq.gz VALIDATION_STRINGENCY=LENIENT

• for bioinformatics questions, you'd better ask https://www.biostars.org/ or http://seqanswers.com/forums/search.php?do=getnew

Answer 2

Try with :

java -jar /opt/picard-tools/picard.jar SamToFastq \ 'I=chr2chr3.bam' \ FASTQ=chr2chr3.f1.fastq \ SECOND_END_FASTQ=chr2chr3.f2.fastq