After consulting with Dr. Bergholz, I discovered that I had not properly converted my .sra files to .fastq files. This is because all of the .sra files that I am using are paired end reads and need to be split up. Right now all my .fastq files contain both forward and reverse reads in one file and I wont be able to use it. So, I deleted all of the previously converted .fasta files and will try it again.
After consulting the sra handbook (and sra forums), I discovered I needed to use the --split-3 option to split my paired end reads when converting them to .fastq format.
So, in the the terminal, I navigated to where my .sra files were located and after much trial and error, I used this command below:
$ /Users/Elliott/sratoolkit.2.4.5-2-mac64/bin/fastq-dump --split-3 ERR274125.sra -O /Users/Elliott/ncbi/public/fastq
This command converted my ERR274125.sra file to two .fastq files and placed it into my fastq folder. The "-O /Users..." was to tell it where to put the .fastq file once it had been generated. I chose to use ERR274125.sra as a test file and the process seemed to work.
I then wanted to do this with all the .sra files and replaced the ERR274125.sra in the above command with just *.sra and hit enter... and it appeared to be working until I got this error:
fastq-dump(573,0x7fff7544f310) malloc: *** error for object 0x1021e6fb0: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
Abort trap: 6
Which I have no idea what it means. I will have to work on trouble shooting a bit more.
//EWW
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