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Old 02-07-2017, 02:22 AM   #1
sasa_k
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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
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Old 02-07-2017, 05:30 AM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

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

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