使用bowtie2比对遇到的问题及解决

一、从ncbi成功下载.src文件，解包出现问题：

vip41@VM-0-15-ubuntu:~/ncbi/public/sra$ fastq-dump SRX4545571.sra 
2018-12-10T12:19:00 fastq-dump.2.3.5 err: column undefined while opening cursor within virtual database module - failed to resolve column 'READ' idx '1'
2018-12-10T12:19:00 fastq-dump.2.3.5 err: column not found while opening table within short read archive module - failed SRX4545571.sra
2018-12-10T12:19:00 fastq-dump.2.3.5 err: column undefined while opening cursor within virtual database module - failed to resolve column 'NAME' idx '3'

=============================================================
An error occurred during processing.
A report was generated into the file '/home/vip41/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

两种类型错误：
1.column undefined while opening cursor within virtual database module - failed to resolve column 'READ' idx '1'

---

2.column not found while opening table within short read archive module - failed SRX4545571.sra
谷歌得到几种解决办法：

第一种。指定参数-A，尝试仍然无法解决。
第二种，全路径调用，尝试，没有反应，太耗时，直接CTRL c 终止了。
第三种，升级fastq-dump到最新版本，目前我的版本：

vip41@VM-0-15-ubuntu:~/ncbi/public/sra$ fastq-dump --version
fastq-dump : 2.3.5

尝试更新到最新版本2.9.2.

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