Deleted:Error in pipe output to samblaster from bwa-mem2
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5 months ago
Adham • 0

Hi,

I am trying to upgrade my command from bwa to bwa-mem2. This command usually works.

bwa mem -M -R "@RG\tID:id\tSM:sample\tLB:lib" human_g1k_v37.fasta sample.1.fq sample.2.fq \ | samblaster -M --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \ | samtools view -S -b - \ > sample.bam

Once I start using bwa-mem2, the piping breaks.

bwa-mem2 mem -M -R "@RG\tID:id\tSM:sample\tLB:lib" human_g1k_v37.fasta sample.1.fq sample.2.fq \ | samblaster -M --excludeDups --addMateTags --maxSplitCount 2 --minNonOverlap 20 \ | samtools view -S -b - \ > sample.bam

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout
Executing in AVX2 mode!!
SA compression enabled with xfactor: 8
[E::bwa_set_rg] no ID at the read group line
Important parameter settings:
BATCH_SIZE: 512
MAX_SEQ_LEN_REF: 256
MAX_SEQ_LEN_QER: 128
MAX_SEQ_LEN8: 128
SEEDS_PER_READ: 500
SIMD_WIDTH8 X: 32
SIMD_WIDTH16 X: 16
AVG_SEEDS_PER_READ: 64
samblaster: Input file is empty. Exiting.
samblaster: Premature exit (return code 1).

Do you have any idea to run samblaster from bwa-mem2 ?? Thanks !

mapping markduplicate bwa-mem2 samblaster • 515 views
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