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fast-dump error, SRA Toolkit is Updated???
0
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2.9 years ago
oars • 150
@oars41179

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.

SRA toolkit fastq-dump • 1.7k views
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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
Entering edit mode
2.9 years ago
genomax 68k
@genomax

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
ATGATATAAACTGGCTCATTTGATGCCAAGACTGACCATCACCACCATACCAAGGTCATCACTGATCAGAGGCCTAACCCAAGGAGGGGGTCATGTGCAG
?@@DA??D?FHFHIDGBGHFHC<HH@DHDCEFFCB@GG?CBCGDBGGF9?FCH@?F<BGHIGB@FHIIGE;DG5?EAEEED?A=;;?BB/<0ACCDCCC:
ACTCTCAAGTGGACGGGGTCCCATTTGCACAGGGGGAGACCTTACAGCCTACGTTGAGTCTATACTTACCACTTAGTGAGCATNNNNNNNNNNNNNNNNN
@<@DDDDD?FFAFIF>E@E1))?EDGFIECBG96??@5@@;=CEFF>E=AB;9;>=?A;>@AA@BDB<>B>A?BB>:@>ABBB#################

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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?

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

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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!