[mira_talk] (no subject)
- From: Rob Good <rtgood@xxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 11 Feb 2011 10:56:52 +1100
I'm trying to assemble 5 million solexa reads against a drosophila ref.
mira -fastq -job=mapping,genome,accurate,solexa -project=DGRP-712
I get an unceremonious killed with no log output apart from what's on the
screen.
I only have 12 Gb RAM but thought I'd try it after reading the optimistic words
from Bastein on 3.2.1.5 regarding memory improvements
Am I being too hopeful
Done.
Loaded 15 reads with 168736537 raw bases.
0 reads have quality accounted for.
Postprocessing backbone(s) ... this may take a while.
15 to process
2L_bb 23011544
2LHet_bb 368872
2R_bb 21146708
2RHet_bb 3288761
3L_bb 24543557
3LHet_bb 2555491
3R_bb 27905053
3RHet_bb 2517507
4_bb 1351857
M_bb 19517
Uextra_bb 29004656
U_bb 10049037
X_bb 22422827
XHet_bb 204112
YHet_bb 347038
Localtime: Fri Feb 11 09:29:40 2011
Seeing strain 1: "ReferenceStrain"
Generated 1 unique strain ids for 15 reads.
Strain "default" has 0 reads.
Strain "ReferenceStrain" has 15 reads.
Loading data (Solexa) from FASTQ files,
Localtime: Fri Feb 11 09:29:40 2011
Counting sequences in FASTQ file: found 5583864 sequences.
Localtime: Fri Feb 11 09:32:38 2011
Solexa will load 5583864 reads.
Longest Sanger: 0
Longest 454: 0
Longest PacBio: 0
Longest Solexa: 1412
Longest Solid: 0
Longest overall: 1412
Total reads to load: 5583864
-AL:shme is 0, automatically determining optimal value.
set -AL:shme 211
-SB:brl is 0, automatically determining optimal value.
brl: 3246
-SB:bro is 0, automatically determining optimal value.
bro: 1623
Reserving space for reads (this may take a while)
tcmalloc: large alloc 1319575552 bytes == 0x2b8d7b000 @
Reserved space for 5687818 reads (including backbone rails).
Adding rails to 15 contigs (this may take a while).
Killed
[rtgood1@imokurok ~]$ ls
Cheers
Rob
Rob Good
Ph. +61 3 8344 2347
Mob. 0434058250
Genetics Dept
University of Melbourne
PARKVILLE, Australia
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