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MGEScan / mgescan

A Galaxy based system for identifying retrotransposons in genome
http://mgescan.github.io/mgescan/
GNU General Public License v3.0
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CalledProcessError : couldn't open /home/maybelinot/home_prj/mgescan/output.1/ltr/ltr/chr6.fa.ltr0 #13

Open maybelinot opened 8 years ago

maybelinot commented 8 years ago

When I run the mgescan on chr6 GRCh38/hg38 got following error, probably there is some issue with rights on file creation, but I'm not sure..

(mgescan)[maybelinot@dhcp-24-108 mgescan]$ mgescan ltr ./input/
MGEScan environment variable is not defined or .mgescanrc is not sourced.
/home/maybelinot/mgescan3 (default path) is used to run MGEScan
ltr: starting
Returned 0
Finding LTRs
Finding MEM
Making bin
Finding putative ltr
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6260000 6270000 6280000 6290000 6300000 6310000 6320000 6330000 6340000 6350000 6360000 6370000 6380000 6390000 6400000 6410000 6420000 6430000 couldn't open /home/maybelinot/home_prj/mgescan/output.1/ltr/ltr/chr6.fa.ltr0
Process Process-1:
Traceback (most recent call last):
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "build/bdist.linux-x86_64/egg/mgescan/cmd.py", line 178, in ltr
    res1 = self.run_cmd(cmd1)
  File "build/bdist.linux-x86_64/egg/mgescan/cmd.py", line 225, in run_cmd
    retcode = check_call(cmd.split())
  File "/usr/lib64/python2.7/subprocess.py", line 540, in check_call
    raise CalledProcessError(retcode, cmd)
CalledProcessError: Command '['/home/maybelinot/mgescan3/src/mgescan/ltr/find_ltr.pl', '-genome=/home/maybelinot/home_prj/mgescan/input/divided-genome', '-data=/home/maybelinot/home_prj/mgescan/output.1', '-hmmerv=3', '-min_dist=2000', '-max_dist=20000', '-min_len_ltr=130', '-max_len_ltr=2000', '-ltr_sim_condition=70', '-cluster_sim_condition=70', '-len_condition=70']' returned non-zero exit status 2