命令行compliation错误

Question

遇到一个单线的问题......

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

[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$ 

完成了一些阅读，但努力寻找运行此命令的解决方案 - 认为它与命令的-R选项部分中的嵌套'有关......有没有办法逃避这些？< / p>

Answer 1

Perl没有sys function。你的意思是system吗？

此外，语法高亮显示是正确的引用。 R'@RG中的单引号结束了第一个单引号字符串，这似乎不正确。