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Old 02-07-2017, 01:22 AM   #1
Junior Member
Location: Europe

Join Date: Feb 2017
Posts: 1
Default fastq-dump problem

Hi all!

I'm trying to run fastq-dump on a cluster I never worked before and it doesn't work.
On the other cluster - never had problems.

Have you ever seen such error message?

> fastq-dump $working_folder/$name_run
2017-02-07T10:19:21 fastq-dump.2.1.9 err: path not found while loading dynamic library within file system module - failed to open SRA manager
Written 0 spots total

I have no idea what it means and nowhere in Google can I find this error message.

The module is installed:
Currently Loaded Modules:
1) term_color
2) resources
3) std_env
4) GCC/4.7.2
5) hwloc/1.6.2-GCC-4.7.2
6) OpenMPI/1.6.4-GCC-4.7.2
7) gompi/1.4.10
8) OpenBLAS/0.2.6-gompi-1.4.10-LAPACK-3.4.2
9) FFTW/3.3.3-gompi-1.4.10
10) ScaLAPACK/2.0.2-gompi-1.4.10-OpenBLAS-0.2.6-LAPACK-3.4.2
11) goolf/1.4.10
12) bzip2/1.0.6-goolf-1.4.10
13) Boost/1.51.0-goolf-1.4.10
14) zlib/1.2.8-goolf-1.4.10
15) NCBI-Toolkit/9.0.0-goolf-1.4.10

Thanks for any help!!
sasa_k is offline   Reply With Quote
Old 02-07-2017, 04:30 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076

What version of SRAtoolkit are you running? NCBI recently switched to using https-only connections. If you are not running the latest version of SRAtoolkit then that would be the first thing to check.
GenoMax is offline   Reply With Quote

environment error, error, fastq-dump, sra conversion, sra fastq error

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