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[软件] 求助CentOS服务器上Cuffmerge的环境搭建及使用

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发表于 2015-7-14 14:10:58 | 显示全部楼层 |阅读模式
20金钱
问题1:
       由于不是系统管理员,并没有权限修改环境变量,故而cufflinks下的软件只能通过绝对路径来访问
调用Cuffmerge的时候可以手动输入,但Cuffmerge的程序内部自动调用cuffcompare以及gtf_to_sam等命令时默认是相对路径调用的
因此我通过vi命令将每个命令的绝对路径添加到Cuffmerge的源代码中............................不知道这样会不会引起软件运行异常甚至报错。
(ps:就目前而言,修改代码后并没有出现原来的 cuffcompare can not found 之类的错误)






问题2:
       ①由于操作的是人类全基因组,大概是对UCSC不太熟悉的缘故,并没有找到hg_19有效的 的gtf注释文件,不知道该文件的缺省是否会影响Cuffmerge的运行结果?




       ②在网上通过查找发现Cuffmerge的命令中还需要基因组 fq 文件作为参考,在这里想问问,如果我的数据是十个实验对象的全基因组文件,每个对象都有正反测序两个fq文件
          那么在Cuffmerge的命令中应该怎样将其作为参考基因组文件?是放在一个文件夹下就可以了么?这样的参考文件是否是必须的?




       ③这也是我当前无法解决的问题,指令、运行过程、报错信息如下:

[chenjx@localhost chenjh]$ /home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cuffmerge -p 32 assembiles.txt

[Tue Jul 14 13:24:25 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Jul 14 13:24:25 2015] Preparing output location ./merged_asm/
Warning: no reference GTF provided!
[Tue Jul 14 13:25:30 2015] Converting GTF files to SAM
[13:25:31] Loading reference annotation.
[13:26:21] Loading reference annotation.
[13:26:33] Loading reference annotation.
[13:26:45] Loading reference annotation.
[13:26:54] Loading reference annotation.
[13:27:09] Loading reference annotation.
[13:27:14] Loading reference annotation.
[13:27:20] Loading reference annotation.
[13:27:27] Loading reference annotation.
[13:27:32] Loading reference annotation.
[Tue Jul 14 13:27:49 2015] Assembling transcripts
Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu).
Command line:
/home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cufflinks -o ./merged_asm/ -F 0.05 -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 32 ./merged_asm/tmp/mergeSam_fileKuqahG
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileKuqahG doesn't appear to be a valid BAM file, trying SAM...
[13:31:00] Inspecting reads and determining fragment length distribution.
Processed 30915 loci.
> Map Properties:
>       Normalized Map Mass: 538969.00
>       Raw Map Mass: 538969.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[13:31:16] Assembling transcripts and estimating abundances.
Processed 31016 loci.
[Tue Jul 14 13:32:14 2015] Comparing against reference file None
/bin/sh: cuffcompare: command not found
        [FAILED]
Error: could not execute cuffcompare
Traceback (most recent call last):
  File "/home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 580, in ?
    sys.exit(main())
  File "/home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 559, in main
    compare_meta_asm_against_ref(params.ref_gtf, params.fasta, output_dir+"/transcripts.gtf")
  File "/home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 406, in compare_meta_asm_against_ref
    tmap = compare_to_reference(gtf_input_file, ref_gtf, fasta_file)
  File "/home/chenjx/Desktop/software/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 342, in compare_to_reference
    exit(1)
TypeError: 'str' object is not callable
      


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