命令是根据我自己的样本名字改的：bwa mem  $BWA_INDEX  $workdir/2.data_qc/${i}.man_1.clean.fastq \

    $workdir/2.data_qc/${i}.man_2.clean.fastq -t 2 -M \

     -R "@RG\tID:${i}\tLB:${i}\tPL:ILLUMINA\tSM:${i}" \

      |samtools view -bS -h - > $workdir/3.map/bwa/${i}.bam

出现：[M::bwa_idx_load_from_disk] read 0 ALT contigs

[M::process] read 206690 sequences (20000138 bp)...

[M::process] read 206798 sequences (20000039 bp)...

[W::sam_hdr_create] Ignored @SQ SN:VBZB010 : bad or missing LN tag

[E::sam_hrecs_update_hashes] Header includes @SQ line "VBZB010" with no LN: tag

samtools view: failed to add PG line to the header

但grep   .fa文件后。

1到>29 dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:29:1:46153303:1 REF

>X dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:X:1:136336377:1 REF

>Y dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:Y:1:26357969:1 REF

>VBZB01000077.1 dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:VBZB01000077.1:1:270566:1 REF

>VBZB01000078.1 dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:VBZB01000078.1:1:243958:1 REF

>VBZB01000079.1 dna:primary_assembly primary_assembly:LU_Bosgru_v3.0:VBZB01000079.1:1:200048:1 REF

下面还有很多VBZB开头的

这是怎么回事呢？应该怎么结解决呢？谢谢老师了！