dmnfarrell / smallrnaseq

small rna-seq analysis package
GNU General Public License v3.0
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libblastinput.sp issue #10

Open RNJ1993 opened 3 years ago

RNJ1993 commented 3 years ago

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