This is a test version of Biostars. For the public version, visit https://www.biostars.org.
fast-dump error, SRA Toolkit is Updated???

I'm having a problem with the following command:

fastq-dump --split-files --origfmt SRR1611183

Here is the error message:

2018-03-06T01:50:18 fastq-dump.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed 
to resolve accession 'SRR1611183' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )
Redirected!!!
2018-03-06T01:50:18 fastq-dump.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2018-03-06T01:50:18 fastq-dump.2.3.5 err: item not found while constructing within virtual database module - the path 'SRR1611183' cannot be opened as database or table

I've researched the issue on the web and the consensus was that I needed to update my sra toolkit to the latest version 2.9.0 (so I did); however, I'm still getting the same error message?

Some more troubleshooting, I type in the following:

$ which fastq-dump

and get...

/usr/bin/fastq-dump

Then I try a test from the github instructions:

fastq-dump --stdout SRR390728 | head -n 8

and get the same error...

:-(

I guess I could just download the data directly from EMBL-EBI (https://www.ebi.ac.uk/ena/data/view/SRR1611183) but I really want to figure this one out.

fastq-dump sratoolkit
• 6,722 views • link
updated by Ram Ram • written by oars oars

Thanks - I don't understand why I'm all the sudden having issues. I was able to run this command with no problems last month?

• 0 views • link
written by oars oars

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

• 0 views • link
written by GenoMax GenoMax

I am able to replicate the error using an older version of fastq-dump version 2.5.2. However, the newer version of the fastq-dump (2.9.0) works fine.

• 0 views • link
written by Sej Modha Sej Modha

I am not sure what happened to my previous but it seems to have disappeared.

I was able to replicate the error using an older version of the fastq-dump (2.5.2), however, newer version of the fastq-dump (v2.9.0) works just fine.

• 0 views • link
written by Sej Modha Sej Modha

1 answer

fastq-dump --split-files -F -Z -X 5 SRR1611183

Works for me using v.2.8.2. 

Read 5 spots for SRR1611183
Written 5 spots for SRR1611183
@11V6WR1:158:H0AVAADXX:1:1101:1160:2147
ATGATATAAACTGGCTCATTTGATGCCAAGACTGACCATCACCACCATACCAAGGTCATCACTGATCAGAGGCCTAACCCAAGGAGGGGGTCATGTGCAG
+11V6WR1:158:H0AVAADXX:1:1101:1160:2147
?@@DA??D?FHFHIDGBGHFHC<HH@DHDCEFFCB@GG?CBCGDBGGF9?FCH@?F<BGHIGB@FHIIGE;DG5?EAEEED?A=;;?BB/<0ACCDCCC:
@11V6WR1:158:H0AVAADXX:1:1101:1160:2147
ACTCTCAAGTGGACGGGGTCCCATTTGCACAGGGGGAGACCTTACAGCCTACGTTGAGTCTATACTTACCACTTAGTGAGCATNNNNNNNNNNNNNNNNN
+11V6WR1:158:H0AVAADXX:1:1101:1160:2147
@<@DDDDD?FFAFIF>E@E1))?EDGFIECBG96??@5@@;=CEFF>E=AB;9;>=?A;>@AA@BDB<>B>A?BB>:@>ABBB#################
• 0 views • link
written by GenoMax GenoMax

Thanks - I don't understand why I'm all the sudden having issues. I was able to run this command with no problems last month?

• 0 views • link
written by oars oars

Have you tried re-running vdb-config utility to set paths for temp directory (and any other options)?

• 0 views • link
written by GenoMax GenoMax

I looked in to the feature but my directory should be ok, I have 80 GB of free space and only need ~ 15GB. I'll try again and report back.

edit - I ended up removing and purging the entire sra toolkit and then re-installing from scratch, starting with the wget function.

I'm happy to report that it seems to have done the trick!

• 0 views • link
written by oars oars

Log in to answer this question.

More posts like this