I am already in the directory where I stored all the files and then exceuted fasq-dump..is it right?
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Originally posted by dena.dinesh View PostI am already in the directory where I stored all the files and then exceuted fasq-dump..is it right?Last edited by GenoMax; 11-06-2014, 05:28 AM.
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I tried giving relative path. then also the same error..how can i rectify it.Last edited by dena.dinesh; 11-06-2014, 07:05 AM.
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Dear Kruger,
Did it ran well for you? When I ran fastq-dump ./SRR1266967.sra, it failed immeditely where as for other files it ran for 3 seconds and throwed this error.Last edited by dena.dinesh; 11-06-2014, 07:05 AM.
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Hi
I am using fastqdump 2.1.7. I downloaded the sratoolkit.2.4.2-ubuntu64 and later installed it suing sudo agt-get command. Inside the bin folder of sratoolkit.2.4.2 I am able find following version fastq-dump version:
fastq-dump.2.4.2; fastq-dump; fastq-dump.2
But I am not able to run the fastq-dump.2.4.2. Not only this file but also all other files of version 2.4.2 were higlighted in green color and I am not able to run those highlighted in green color.
Please guide me.
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Originally posted by dena.dinesh View PostHi
I am using fastqdump 2.1.7. I downloaded the sratoolkit.2.4.2-ubuntu64 and later installed it suing sudo agt-get command. Inside the bin folder of sratoolkit.2.4.2 I am able find following version fastq-dump version:
fastq-dump.2.4.2; fastq-dump; fastq-dump.2
But I am not able to run the fastq-dump.2.4.2. Not only this file but also all other files of version 2.4.2 were higlighted in green color and I am not able to run those highlighted in green color.
Please guide me.
Code:$ chmod u+x fastq-dump*
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Originally posted by dena.dinesh View PostWhen I ran fastq-dump ./SRR1266967.sra, it failed immeditely
Code:wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR126/SRR1266967/SRR1266967.sra md5sum SRR1266967.sra 01c653175917848a60ad01f700793a49 SRR1266967.sra fastq-dump -F SRR1266967.sra grep ^@ SRR1266967.fastq | wc 16557954 16557954 521453404
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I had a similar error message. The problem in my case was that the temporary download directory was full. I resolved it by changing the download directory using vdb-config -i.
From: http://trace.ncbi.nlm.nih.gov/Traces..._doc&f=std#s-3
The default location for the "download repository" is:
Linux: /home/[user_name]/ncbi/public
Mac OS X: /Users/[user_name]/ncbi/public
Windows: C:\Users\[user_name]\ncbi\public
Here's hoping for some more helpful error messages in the next release!
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