命令行遵从性错误

Question

一个班轮遇到了一些问题..。

ls *.fq.gz | cut -f 1 -d . | uniq | perl -pe 'chomp; system "bwa-0.7.9a mem  -M /refs/GATK_bundle_2.3//human_g1k_v37.fasta -R'@RG\tID:Foo\tSM:bar' $_.1.fq.gz $_.2.fq.gz > $_.sam"'

输出是

[E::bwa_set_rg] the read group line is not started with @RG
CLMP10920-1[E::bwa_set_rg] the read group line is not started with @RG
CLMP10920-2[E::bwa_set_rg] the read group line is not started with @RG
CLMP10920-3[E::bwa_set_rg] the read group line is not started with @RG
CLMP10920-4W[E::bwa_set_rg] the read group line is not started with @RG
COL1A110908-1[E::bwa_set_rg] the read group line is not started with @RG
COL1A110908-2[E::bwa_set_rg] the read group line is not started with @RG
COL1A110908-3[E::bwa_set_rg] the read group line is not started with @RG
COL1A110908-4Wgleadalln@mgcl01:~/testing/analysis$ 

进行了一些阅读，但很难找到运行此命令的解决方案--认为它与命令的-R选项中的嵌套‘有关.有办法逃过这些吗？

Answer 1

Perl没有sys 函数。你是说系统吗

另外，语法高亮符对于引号是正确的。R'@RG中的引号结束了第一个单引号字符串，这似乎不正确。