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libblastinput.sp issue #10

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RNJ1993 opened this issue Jun 18, 2021 · 0 comments
Open

libblastinput.sp issue #10

RNJ1993 opened this issue Jun 18, 2021 · 0 comments

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@RNJ1993
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RNJ1993 commented Jun 18, 2021

Hi, I have been running smallrnaseq with the default.conf options selected to run novel miRNA detection from the reference genome.

I keep getting this error - any ideas?

makeblastdb: error while loading shared libraries: libblastinput.so: cannot open shared object file: No such file or directory
Traceback (most recent call last):
File "/snap/smallrnaseq/3/bin/smallrnaseq", line 11, in
load_entry_point('smallrnaseq==0.5.0', 'console_scripts', 'smallrnaseq')()
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/app.py", line 504, in main
W.run()
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/app.py", line 101, in run
self.map_mirnas()
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/app.py", line 217, in map_mirnas
cpus=self.cpus)
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/novel.py", line 727, in find_mirnas
new = find_from_known(new, species)
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/novel.py", line 760, in find_from_known
utils.make_blastdb('temp.fa', title='mirbase-temp')
File "/snap/smallrnaseq/3/lib/python3.5/site-packages/smallrnaseq/utils.py", line 142, in make_blastdb
result = subprocess.check_output(cmd, shell=True, executable='/bin/bash')
File "/snap/smallrnaseq/3/usr/lib/python3.5/subprocess.py", line 626, in check_output
**kwargs).stdout
File "/snap/smallrnaseq/3/usr/lib/python3.5/subprocess.py", line 708, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'makeblastdb -in temp.fa -dbtype nucl -out mirbase-temp' returned non-zero exit status 127

thanks

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