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4 hours ago by

After performing a blastn search against an SRA accession, I want to retrieve several dozen matching reads using SRA Toolkit. As a test, I tried this command to get one of the matching reads:

fastq-dump  --split-spot  SRR10201511.86616936.2

The expected result was a fastq file like this:

@SRR10201511.86616936.1 86616936 length=151 ATAATAAGAAAGCTGTAATGAAAATAGCCCAAACGAATAAAGGCTGTCTCTTATACACATCTAAAATATTTTTTATTAACTTAAATTAAAAAGCGAATAAAATTAAGAAAGCAATCATTAAACAGAATAAAGCAATAGATTCAGTTAAAGC
+SRR10201511.86616936.1 86616936 length=151 
AAFFFJJJJJJJJFJJFJJJFJJJJJJJJJJFJJJJFFJJJJJJFJJJJJJJJJJJJJJJJFJJJFJJJFJAJJJJFJFJJJJJJFAJAJJJF7AAJJFJJJJJJJJJJJFJFJJJJJJJJJJJ<FJ7JFFFJFJFJJJJF-<77AFFJAA 
@SRR10201511.86616936.2 86616936 length=151 
ACATAATATGTTATTACAATCTGCAAAATTTATTGGTGCTGGATTAGCTACTATTGGATTAGCAGGTGCTGGTATCGGTATCGGTTCAGTATTTAGTTCATTAGTTTTAGGTATTTCTAGAAACCTTTCTTTACAACAAGATNNNNNNNNN
+SRR10201511.86616936.2 86616936 length=151 
AAFFFJFF7AJJJJFJJJJJFJJJJJJFJJFJFJJFJFFJJAJJJJJJFFJJFJJJFJJJJ7JFJJF<AJJAJFJJFJJJJ<JJFFFJJJJJJJJFFAJJJJJ<J-7JJJJF-<FFJJJFJAAF<-AFJFJJJJF<FF-7<F#########

But instead I retrieved thousands of reads in a ~3 GB file. The first read looks like this:

@SRR10201511.86616936.2.1 1 length=151
NTTCAGCCTTGCGACCATACTCCTGTCTCTTATACACATCTAGATGTGTATAAGAGACAAGTACTAATACAGCAAAAAGACTTGTGCGATTTTTCAAGCGCAGCAACAACCACTGGCAAAGACCCCAACAGGAAGAAAGACTATAAGATCG
+SRR10201511.86616936.2.1 1 length=151
#AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFJFJJJJJJJJJFJJJJJJJJJJ<JJJJJJJJJJJJJJJJJFF<AFAFFJJAAA---FAJJFJFF<FJFFF7--F---7FA<7F--))7A)--7AA<AFA-7----7A-<-<-
@SRR10201511.86616936.2.1 1 length=151
NAAAGTCTTTCTTCCTGTTAGAGTCTTTGCCAGTGGTTGTTGCTGCGCTTGAAAAATCGCACAAGTCTTTTTGCTGTATTAGTACTTGTCTCTTATACACATCTAGATGTGTATAAGAGACAGGAGAATGGTCGCAAGGCTGNNNNNNNNN
+SRR10201511.86616936.2.1 1 length=151
#AAFFJJJJJJJJ<FFJ-FJJJJ<<FJJJJFJJJJJ7FJJJJJ-FJJJ7AFJJJJJJJJJJJJJJFJFFJ-A<J7A<AFJJJJJJJFJ7FAF<FJA7FJAJ--A7<--7-7-<7FAAAFJJJF7JJ-7-7--<<-7FJ77--#########

Why am I not retrieving the desired, single read with fastq-dump?



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