Hello,
I am a newbie to using AllPaths and I ran into an error while running the RunallPathsLG algorithm.
After preparing the input files, and halfway through running the RunAllPathsLG command I get an error message with the following output:
------------------ FindErrors -> frag_reads_edit.fastb
290282408 total number of original fragment reads
96.2 mean length of original fragment reads in bases
38.8 % gc content of fragment reads
0.2 % of bases pre-corrected
2299242576 estimated genome size in bases
21.0 % genome estimated to be repetitive (at K=25 scale)
9 estimated genome coverage by fragment reads
0.32 estimated standard deviation of sequencing bias (at K=25 scale)
92.7 % of bases confirmed in cycle 0
1.32 % of bases corrected in cycle 0
0.01 % of bases with conflicting corrections in cycle 0
94.8 % of bases confirmed in cycle 1
0.31 % of bases corrected in cycle 1
0.01 % of bases with conflicting corrections in cycle 1
------------------ CleanCorrectedReads -> frag_reads_corr.25mer.kspec
8.1 % of reads removed because of low frequency kmers
------------------ FillFragments -> filled_reads.fastb
58.1 % of fragment pairs that were filled
------------------ Memory and CPU usage
64 available cpus
126.1 GB of total available memory
389.0 GB of available disk space
50.87 hours of total elapsed time
46.76 hours of total per-module elapsed time
596678.04 hours of total per-module user time
12759.45 effective parallelization factor
115.56 GB memory usage peak
Run directory: /archive/REFERENCE/DATA/RUN
Log directory: /archive/REFERENCE/make_log/DATA/RUN/SUBDIR/2013-05-10T07:55:31
*** Make encountered an error, see above for error messages. ***
I am not really sure as to where I would look for any error's. Since the makefile is generated before the actual process, I do not really understand where the error is. Has anyone encountered something like this before/does anyone have any suggestions?
I did post the same question in the allpaths-user forum, but I havent got any reply yet.
Any insights would be greatly appreciated.
Thanks in advance for your time.
Best,
Akshaya
I am a newbie to using AllPaths and I ran into an error while running the RunallPathsLG algorithm.
After preparing the input files, and halfway through running the RunAllPathsLG command I get an error message with the following output:
------------------ FindErrors -> frag_reads_edit.fastb
290282408 total number of original fragment reads
96.2 mean length of original fragment reads in bases
38.8 % gc content of fragment reads
0.2 % of bases pre-corrected
2299242576 estimated genome size in bases
21.0 % genome estimated to be repetitive (at K=25 scale)
9 estimated genome coverage by fragment reads
0.32 estimated standard deviation of sequencing bias (at K=25 scale)
92.7 % of bases confirmed in cycle 0
1.32 % of bases corrected in cycle 0
0.01 % of bases with conflicting corrections in cycle 0
94.8 % of bases confirmed in cycle 1
0.31 % of bases corrected in cycle 1
0.01 % of bases with conflicting corrections in cycle 1
------------------ CleanCorrectedReads -> frag_reads_corr.25mer.kspec
8.1 % of reads removed because of low frequency kmers
------------------ FillFragments -> filled_reads.fastb
58.1 % of fragment pairs that were filled
------------------ Memory and CPU usage
64 available cpus
126.1 GB of total available memory
389.0 GB of available disk space
50.87 hours of total elapsed time
46.76 hours of total per-module elapsed time
596678.04 hours of total per-module user time
12759.45 effective parallelization factor
115.56 GB memory usage peak
Run directory: /archive/REFERENCE/DATA/RUN
Log directory: /archive/REFERENCE/make_log/DATA/RUN/SUBDIR/2013-05-10T07:55:31
*** Make encountered an error, see above for error messages. ***
I am not really sure as to where I would look for any error's. Since the makefile is generated before the actual process, I do not really understand where the error is. Has anyone encountered something like this before/does anyone have any suggestions?
I did post the same question in the allpaths-user forum, but I havent got any reply yet.
Any insights would be greatly appreciated.
Thanks in advance for your time.
Best,
Akshaya
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