tophat 运行报错

更新samtools 后 运行 TopHat v2.0.9 报错:

[2015-09-15 15:50:07] Beginning TopHat run (v2.0.9)

———————————————–

[2015-09-15 15:50:07] Checking for Bowtie

Bowtie version: 2.1.0.0

[2015-09-15 15:50:08] Checking for Samtools

Traceback (most recent call last):

File “/software/biosoft/bin/tophat”, line 4072, in <module>

sys.exit(main())

File “/software/biosoft/bin/tophat”, line 3874, in main

check_samtools()

File “/software/biosoft/bin/tophat”, line 1552, in check_samtools

samtools_version_str, samtools_version_arr = get_samtools_version()

File “/software/biosoft/bin/tophat”, line 1534, in get_samtools_version

samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]

AttributeError: ‘NoneType’ object has no attribute ‘group’

原因：tophat 2.0.13 以下版本需要依赖samtools, 并且版本不能太高。

解决办法：

1. 安装 samtools v1.0 以下版本（不包括v 1.0）
2. 安装 tophat 2.0.13及其以上版本,并使用tophat2命令（因为tophat命令默认没有预先打包samtools）

总结于官网提示：http://ccb.jhu.edu/software/tophat/tutorial.shtml

Note: Starting with version 2.0.13 TopHat no longer requires the user to have the SAMtools library (libbam.a), headers or even the samtools program installed, as TopHat2 comes pre-packaged with a stable version of SAMtools which is known to work well with TopHat. Also, TopHat uses the SeqAn library that comes with the TopHat2 source code distribution. It is not necessary for the SeqAn library to be installed separately in order to run TopHat.

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