fastq-dump 报错 解决方案

命令行:

~/sratoolkit/sratoolkit.2.3.2/bin/fastq-dump --split-spot --gzip xxxx.sra

报错信息:

fastq-dump.2.3.2 err: name not found while resolving tree within virtual file system module - failed to open 'xxxx.sra'

解决方法:

找不到xxx.sra,就给它全路径就可以了

the problem happens when you use a local path for the SRA file. Try using the absolute path! fastq-dump /data/etc/SRR00000.sra should do the trick

 

http://seqanswers.com/forums/showthread.php?t=29447

 

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报错信息:

connection busy while validating within network system module

方法1:

Add sratoolkit to environment variables


EXPORT PATH=$PATH:/path/to/sratoolkit/bin/ /path/to/sratoolkit/bin/fastq-dump --split-3 filename.sra


方法2:

Just get the fastq from EBI: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR375/ERR375895/ERR375895.fastq.gz

 

 

posted @ 2013-10-03 11:07  emanlee  阅读(8801)  评论(0编辑  收藏  举报