Hi all,
I was trying to align two versions of human chromosome I (GenBank
entry and a fasta sequence from an assembly) using progressive mauve.
The .sslist files (1,026,186 KB each) were created, along with the
beginning of the .guide_tree file, which contains a single line:
(seq2,seq1);
but the program then terminated. Here is the log:
OS name is: Windows 7 arch: amd64
Executing:
win64\progressiveMauve --output=C:\Users\plunkettg\durfee --output-guide-tree=C:\Users\plunkettg\durfee.guide_tree --backbone-output=C:\Users\plunkettg\durfee.backbone C:\Users\plunkettg\Homo sapiens.NC_000001.9.gbk C:\Users\plunkettg\Chr 1_human_all_SB.fas
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\rawF85C.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Homo sapiens.NC_000001.9.gbk 247249719 base pairs.
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\rawD9A.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Chr 1_human_all_SB.fas 247249719 base pairs.
Using weight 19 mers for initial seeds
Creating sorted mer list
Create time was: 183 seconds.
Creating sorted mer list
Create time was: 181 seconds.
0%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
using default bp penalty: 195170
using default bp estimate min score: 585509
Starting with 1 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0 0
0 0
Writing guide tree to C:\Users\plunkettg\durfee.guide_tree
reading tree...scoring error
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 1 initial LCBs
Executing:
win64\progressiveMauve --output=C:\Users\plunkettg\durfee --output-guide-tree=C:\Users\plunkettg\durfee.guide_tree --backbone-output=C:\Users\plunkettg\durfee.backbone C:\Users\plunkettg\Homo sapiens.NC_000001.9.gbk C:\Users\plunkettg\Chr 1_human_all_SB.fas
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\rawF85C.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Homo sapiens.NC_000001.9.gbk 247249719 base pairs.
Storing raw sequence at C:\Users\PLUNKE~1\AppData\Local\Temp\rawD9A.tmp
Sequence loaded successfully.
C:\Users\plunkettg\Chr 1_human_all_SB.fas 247249719 base pairs.
Using weight 19 mers for initial seeds
Creating sorted mer list
Create time was: 183 seconds.
Creating sorted mer list
Create time was: 181 seconds.
0%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.
using default bp penalty: 195170
using default bp estimate min score: 585509
Starting with 1 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0
0
Writing guide tree to C:\Users\plunkettg\durfee.guide_tree
reading tree...scoring error
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 1 initial LCBs
Exited with error code:
-2147483645
This was reproducible. Any suggestions? The machine has 12 GB of
RAM and 52 GB of free disk space.
Cheers,
Guy
------------------------------------------------------------------------------ What You Don't Know About Data Connectivity CAN Hurt You This paper provides an overview of data connectivity, details its effect on application quality, and explores various alternative solutions. http://p.sf.net/sfu/progress-d2d
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