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Comments (5)

lpryszcz avatar lpryszcz commented on August 29, 2024

It seems your genome (390Mb) is already assembled into 14 chromosomes. Why do you want to use Redundans on it?

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Deeptirao avatar Deeptirao commented on August 29, 2024

redundans_error2

Yes, I made a mistake in the command earlier. My intention was to use the 390 MB genome as a reference. I did run it again with corrections, but the same error appeared even when I did that. Please check the screen shot.

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lpryszcz avatar lpryszcz commented on August 29, 2024

make sure snap-aligner is correctly installed and works (REDUNDANSPATH/bin/snap/snap-aligner)

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lpryszcz avatar lpryszcz commented on August 29, 2024

alternatively use -b to use BWA instead of snap-aligner

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SvitlanaLukicheva avatar SvitlanaLukicheva commented on August 29, 2024

Hello, I have the same issue. Installation of snap-aligner and/or usage of -b option didn't solve the problem.

Traceback (most recent call last):
  File "/CECI/home/ulb/ebe/slukiche/assemblers/redundans/redundans/redundans.py", line 539, in <module>
    main()
  File "/CECI/home/ulb/ebe/slukiche/assemblers/redundans/redundans/redundans.py", line 527, in main
    _check_dependencies(dependencies)
  File "/CECI/home/ulb/ebe/slukiche/assemblers/redundans/redundans/redundans.py", line 441, in _check_dependencies
    p = subprocess.Popen([cmd, '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
  File "/usr/local/python/2.7.3/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/usr/local/python/2.7.3/lib/python2.7/subprocess.py", line 1249, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory```

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