AbstractAlignmentMerger Wrote 0 alignment records and 71729386 unmapped
Hi there,
I am trying to align my fastq data (germline, whole exome sequencing, paired-end with illumina Novaseq). I already did the FastqToSam, MarkIlluminaAdapters and SamtoFastq, but I am having a problem with BWA. I am using version bwa/0.7.17 and reference ucsc.hg19.fasta.
My script is the following:
bwa mem -M -t 7 -p /.../ucsc.hg19.fasta /dev/stdin | java -jar picard.jar MergeBamAlignment ALIGNED_BAM=/dev/stdin UNMAPPED_BAM=sample_fastqtosam.bam OUTPUT=sample_mergebamalignment.bam R=/.../ucsc.hg19.fasta CREATE_INDEX=true ADD_MATE_CIGAR=true CLIP_ADAPTERS=false CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true MAX_INSERTIONS_OR_DELETIONS=-1 PRIMARY_ALIGNMENT_STRATEGY=MostDistant ATTRIBUTES_TO_RETAIN=XS TMP_DIR=/.../TMP
and it gives me this:
INFO AbstractAlignmentMerger Written in coordinate order to output 10,
INFO AbstractAlignmentMerger Written in coordinate order to output 20,
INFO AbstractAlignmentMerger Written in coordinate order to output 30,
INFO AbstractAlignmentMerger Written in coordinate order to output 40,
INFO AbstractAlignmentMerger Written in coordinate order to output 50,
INFO AbstractAlignmentMerger Written in coordinate order to output 60,
INFO AbstractAlignmentMerger Written in coordinate order to output 70,
INFO AbstractAlignmentMerger Wrote 0 alignment records and 71729386 unmap
Can you please help me with this? Thank you in advance.
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