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Hi,
I'm trying to run the example commands and getting the following error:
./pyScaf.py -f test/contigs.reduced.fa -r test/ref.fa -o test/contigs.reduced.ref.fa
Options: Namespace(dotplot='png', fasta='test/contigs.reduced.fa', fastq=None, identity=0.33, joins=5, linkratio=0.7, load=0.2, log=<open file '<stderr>', mode 'w' at 0x7fbd138771e0>, longreads=None, mapq=10, maxgap=0, nofilter_overlaps=False, norearrangements=False, output=<open file 'test/contigs.reduced.ref.fa', mode 'w' at 0x259b4b0>, overlap=0.66, ref='test/ref.fa', threads=4)
maxgap cut-off of 10000 bp
##################################################
[Tue Jan 9 16:18:31 2018][ 9 Mb] Aligning contigs on reference...
##################################################
[Tue Jan 9 16:18:31 2018][ 9 Mb] Saving dotplots to: test/contigs.reduced.fa.png
Traceback (most recent call last):
File "./pyScaf.py", line 1294, in <module>
main()
File "./pyScaf.py", line 1286, in main
s.save(out)
File "./pyScaf.py", line 171, in save
self._get_scaffolds()
File "./pyScaf.py", line 1094, in _get_scaffolds
t2hits, t2size = self._get_hits()
File "./pyScaf.py", line 1035, in _get_hits
dotplot = self.save_dotplot(self.genome, readstdin=True)
File "./pyScaf.py", line 212, in save_dotplot
proc = subprocess.Popen(args, stdin=subprocess.PIPE, stderr=self.log)
File "/home/peter/.pyenv/versions/2.7.6/lib/python2.7/subprocess.py", line 709, in __init__
errread, errwrite)
File "/home/peter/.pyenv/versions/2.7.6/lib/python2.7/subprocess.py", line 1326, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
It doesn't seem to matter whether I build the software from github or use pip/bioconda for installation.
The computer is running Ubuntu 16.04 and python 2.7.6
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