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After almost a full day of fiddling I was able to run transfer_fast5_to_server.py without any errors of missing dependencies. Though, when running the command with all the options I was met with an error.
When I run the command it immediately displays a big block of text (first part) and after a second or two it displays the another text block with a clear indication of an error.
Here is the error (as it's displayed in cygwin, I guess the error part is in the second part of output):
First part
artem@MinION-PC ~
$ ./poreduck/transfer_fast5_to_server.py --reads_dir /cygdrive/f/data/reads --
server_name nshomron --user_name artemd --dest_directory '/groups/nshomron/arte
md/tmp/minion/AlbacoreTest' --sample_name Lambda_Lib7
password:
("Bad option -c.\r\n\r\n\r\nUsage: ping [-t] [-a] [-n count] [-l size] [-f] [-i
TTL] [-v TOS]\r\n [-r count] [-s count] [[-j host-list] | [-k host-li
st]]\r\n [-w timeout] [-R] [-S srcaddr] [-4] [-6] target_name\r\n\r\n
Options:\r\n -t Ping the specified host until stopped.\r\n
To see statistics and continue - type Control-Break;\r\n
To stop - type Control-C.\r\n -a Resolve addresses to host
names.\r\n -n count Number of echo requests to send.\r\n -l size
Send buffer size.\r\n -f Set Don't Fragment flag in packet (I
Pv4-only).\r\n -i TTL Time To Live.\r\n -v TOS Type Of Ser
vice (IPv4-only. This setting has been deprecated\r\n and has
no effect on the type of service field in the IP Header).\r\n -r count
Record route for count hops (IPv4-only).\r\n -s count Timestamp for cou
nt hops (IPv4-only).\r\n -j host-list Loose source route along host-list (I
Pv4-only).\r\n -k host-list Strict source route along host-list (IPv4-only)
.\r\n -w timeout Timeout in milliseconds to wait for each reply.\r\n -
R Use routing header to test reverse route also (IPv6-only). \r\n
-S srcaddr Source address to use.\r\n -4 Force using IPv4.\r
\n -6 Force using IPv6.\r\n\r\n", '')
Second part
SSH passed
('/groups/nshomron/artemd/tmp', 'if [ -d /groups/nshomron/artemd/tmp ]; then ech
o "PRESENT"; fi\r\r\nif: Expression Syntax.\r\n')
Error, parent directory of /groups/nshomron/artemd/tmp/minion/AlbacoreTest does
not exist
Hope you can help me solve it because it would be unfortunate to throw away all the time spent on the setup.
Thanks.
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