bioinformatics - 尝试从 bwa-mem2 到 samblaster 的管道输出

Question

我正在尝试将我的工作流程从 bwa 升级到 bwa-mem2。该命令通常有效。

/usr/local/bin/bwa mem -K 100000000 -t 4 -Y -R '${readGroup}' ${refFasta} ${F1} ${F2} | \
        /usr/local/bin/samblaster -a --addMateTags | /usr/local/bin/samtools view -b -S /dev/stdin > "${label}.refAlign.bam"

但是，一旦我开始使用 bwa-mem2，管道就会中断。

/usr/local/bin/bwa-mem2 mem -K 100000000 -t 4 -Y -R '${readGroup}' ${refFasta} ${F1} ${F2} | \
        /usr/local/bin/samblaster -a --addMateTags | /usr/local/bin/samtools view -b -S /dev/stdin > "${label}.refAlign.bam"

我得到以下输出：

samblaster: Version 0.1.26
samblaster: Inputting from stdin
samblaster: Outputting to stdout
-----------------------------
Executing in AVX512 mode!!
-----------------------------
Ref file: /storage1/fs1/dspencer/Active/refdata/hg38/bwa-mem2/all_sequences.fa
Entering FMI_search
reference seq len = 6434693835
samblaster: Input file is empty. Exiting.
samblaster: Premature exit (return code 1).
[main_samview] fail to read the header from "/dev/stdin".

我也将 fasta 文件从常规 bwa 索引更改为 bwa-mem2 索引。

标签： bioinformaticssamtools