Question: SRAtoolkit: error while running sam-dump
gravatar for c_u
2.4 years ago by
United States
c_u170 wrote:


I am trying to convert an SRA file to the SAM format, and I am using the following command (Ubuntu 17.04) -

sam-dump --output-file out.sam SRR3031662

But after a while of running, it gave the following error -

2017-09-19T23:21:57 sam-dump.2.8.1 sys: libs/kns/unix/syssock.c:524:KSocketTimedRead: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed )

Does anyone know what the problem is here? Quick Google searches did not find any solutions.

Thanks in advance for any help.

sratoolkit sam sra ncbi • 787 views
ADD COMMENTlink written 2.4 years ago by c_u170

I just ran your command on a Ubuntu 16.04 and I was able to download the file. Maybe something wrong with your computer?

ADD REPLYlink written 2.4 years ago by sridhar56100

Hi, is the command I wrote supposed to involve some kind of download? I thought the command was just supposed to convert a SRA file to SAM format. Also, looking at the error I pasted here, do you have any idea what the problem could be?

ADD REPLYlink written 2.4 years ago by c_u170

Not unless you are providing a pre-downloaded SRA file. The command as written will try to dump the data directly from SRA. Save yourself the trouble and get the fastq files from ENA and then align the data yourself.

ADD REPLYlink written 2.4 years ago by genomax78k

hi, thanks for your comment. Yes, I do have a pre-downloaded SRA file and the error is as shown. Thank you for the link for the SRA file (I had downloaded it from the corresponding GEO file). How do you suggest I should align the data myself? I am a complete beginner in this.

ADD REPLYlink written 2.4 years ago by c_u170
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