Redirect cached output on gnu/linux server
by jamdoo from LinuxQuestions.org on (#6QP4G)
I am using a linux server:
Code:Linux g-12-l0002 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/LinuxI have a large data allocation in a specific folder on the server (data_dir), but my home directory is limited to 10GB (home_dir).
There is a program I am trying to use (ksnp v4.1) but it places cached files in home_dir. This rapidly fills up and the program stops. The main output of the program goes to my data_dir. Is it possible to direct the program to output the cached files to my data_dir? I don't have sudo rights on the server.
Here is how the error that is produced during the run:
Code:DEBUG:Cached filtered kmers from kmers.fsplit0 to /home/kSNP/FilteredKmersCache/f9a0efc6f8d763224331f8087822612a86bd118219e4e5f8c001320bc2265537.17.
DEBUG:Cached filtered kmers from kmers.fsplit1 to /home/kSNP/FilteredKmersCache/63a5589a4b6048187c79c26740ee036d2e2b86db4085072b49555020d19be6fb.17.
DEBUG:Cached filtered kmers from kmers.fsplit2 to /home/kSNP/FilteredKmersCache/52c9ce63efc5b9fb5016d6eaf9f6b109a5458a15533bbeae735ceb57a28285a5.17.
Traceback (most recent call last):
File "get_filtered_kmers.py", line 406, in <module>
File "get_filtered_kmers.py", line 330, in cacheFilteredKmers
File "shutil.py", line 418, in copy
File "shutil.py", line 264, in copyfile
OSError: [Errno 28] No space left on device: '/home/kSNP/FilteredKmersCache/52c9ce63efc5b9fb5016d6eaf9f6b109a5458a15533bbeae735ceb57a28285a5.17'
[14629] Failed to execute script 'get_filtered_kmers' due to unhandled exception!
0 GCA_009662435 /data_dir/GCA_009662435.1
1 GCA_009665145 /data_dir/GCA_009665145.2</module>The program is here:
https://sourceforge.net/projects/ksnp/
I ran the program like this:
Code:kSNP4 -in Genome_names_ksnp.txt -k 17 -outdir out_ksnp4Thanks,
James
Code:Linux g-12-l0002 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/LinuxI have a large data allocation in a specific folder on the server (data_dir), but my home directory is limited to 10GB (home_dir).
There is a program I am trying to use (ksnp v4.1) but it places cached files in home_dir. This rapidly fills up and the program stops. The main output of the program goes to my data_dir. Is it possible to direct the program to output the cached files to my data_dir? I don't have sudo rights on the server.
Here is how the error that is produced during the run:
Code:DEBUG:Cached filtered kmers from kmers.fsplit0 to /home/kSNP/FilteredKmersCache/f9a0efc6f8d763224331f8087822612a86bd118219e4e5f8c001320bc2265537.17.
DEBUG:Cached filtered kmers from kmers.fsplit1 to /home/kSNP/FilteredKmersCache/63a5589a4b6048187c79c26740ee036d2e2b86db4085072b49555020d19be6fb.17.
DEBUG:Cached filtered kmers from kmers.fsplit2 to /home/kSNP/FilteredKmersCache/52c9ce63efc5b9fb5016d6eaf9f6b109a5458a15533bbeae735ceb57a28285a5.17.
Traceback (most recent call last):
File "get_filtered_kmers.py", line 406, in <module>
File "get_filtered_kmers.py", line 330, in cacheFilteredKmers
File "shutil.py", line 418, in copy
File "shutil.py", line 264, in copyfile
OSError: [Errno 28] No space left on device: '/home/kSNP/FilteredKmersCache/52c9ce63efc5b9fb5016d6eaf9f6b109a5458a15533bbeae735ceb57a28285a5.17'
[14629] Failed to execute script 'get_filtered_kmers' due to unhandled exception!
0 GCA_009662435 /data_dir/GCA_009662435.1
1 GCA_009665145 /data_dir/GCA_009665145.2</module>The program is here:
https://sourceforge.net/projects/ksnp/
I ran the program like this:
Code:kSNP4 -in Genome_names_ksnp.txt -k 17 -outdir out_ksnp4Thanks,
James