[mira_talk] Fwd: Asking about hybrid assembly

---------- Forwarded message ----------
From: Rafał Woycicki <rafalwoycicki@xxxxxxxxx>
Date: Thu, 23 Jul 2009 22:54:33 +0200
Subject: Fwd: Asking about hybrid assembly
To: bach@xxxxxxxxxxxx

Hi again Bastien,

regarding to my last email I am attaching directory listings:


main directory:
-rw------- 1 ravwoycicki users           0 Jul 21 08:02 EdIt.log
drwx------ 2 ravwoycicki users        4096 Jul 16 13:21 hybrid_d_info
drwx------ 2 ravwoycicki users        4096 Jul 22 05:44 hybrid_d_log
drwx------ 2 ravwoycicki users        4096 Jul 16 13:21 hybrid_d_results
-rw-r--r-- 1 ravwoycicki users  7579123922 Jul 13 23:35 hybrid_in.454.fasta
-rw-r--r-- 1 ravwoycicki users 21968175643 Jul 13 23:35
hybrid_in.454.fasta.qual
-rw-r--r-- 1 ravwoycicki users    60921251 Jul 11 19:03
hybrid_in.sanger.fasta
-rw-r--r-- 1 ravwoycicki users   170083768 Jul 11 19:03
hybrid_in.sanger.fasta.qual
-rw-r--r-- 1 ravwoycicki users  3340616034 Jul 13 23:35
hybrid_traceinfo_in.454.xml
-rw-r--r-- 1 ravwoycicki users    17059740 Jul 11 19:03
hybrid_traceinfo_in.sanger.xml


hybrid_d_log:
-rw------- 1 ravwoycicki users   292832745 Jul 22 05:51
miralog.ads_pass.1.adsfacts.pclusters
-rw------- 1 ravwoycicki users  8574933061 Jul 22 04:39
miralog.ads_pass.1.adsfacts
-rw------- 1 ravwoycicki users         324 Jul 22 04:38
hybrid_int_vectorclip_pass.1.txt
-rw------- 1 ravwoycicki users  2139956348 Jul 22 04:37
miralog.ads_pass.1.complement
-rw------- 1 ravwoycicki users   245313561 Jul 22 04:37
miralog.ads_pass.1.reject
-rw------- 1 ravwoycicki users  2387457140 Jul 21 19:16
miralog.ads_pass.1.forward
-rw------- 1 ravwoycicki users  2576058792 Jul 21 08:02
hybrid_int_posmatchc_preassembly2.0.lst.reduced
-rw------- 1 ravwoycicki users  2859201262 Jul 21 07:58
hybrid_int_posmatchf_preassembly2.0.lst.reduced
-rw------- 1 ravwoycicki users 17191601040 Jul 21 07:12
hybrid_int_normalisedskims_preassembly2.0.bin
-rw------- 1 ravwoycicki users  6239048262 Jul 21 06:11
hybrid_int_posmatchc_preassembly2.0.lst
-rw------- 1 ravwoycicki users  6713522131 Jul 21 06:11
hybrid_int_posmatchf_preassembly2.0.lst
-rw------- 1 ravwoycicki users         529 Jul 21 06:11
hybrid_int_posmatch_megahubs_preassembly2.0.lst
-rw------- 1 ravwoycicki users           0 Jul 20 18:52 miralog.noqualities
-rw------- 1 ravwoycicki users   245114620 Jul 20 18:52 miralog.usedids
-rw------- 1 ravwoycicki users    28691030 Jul 20 18:51
hybrid_info_reads_tooshort
-rw------- 1 ravwoycicki users  1099986479 Jul 20 18:51
hybrid_int_clippings.0.txt
-rw------- 1 ravwoycicki users  6668701216 Jul 20 13:36 hashstat.bin
-rw------- 1 ravwoycicki users 15873626576 Jul 20 07:37 stattmp0.bin
-rw------- 1 ravwoycicki users  6608129872 Jul 20 07:37 stattmp1.bin
-rw------- 1 ravwoycicki users  7601184288 Jul 20 07:37 stattmp2.bin
-rw------- 1 ravwoycicki users 12782374352 Jul 20 07:37 stattmp3.bin
-rw------- 1 ravwoycicki users  8082791232 Jul 20 07:37 stattmp4.bin
-rw------- 1 ravwoycicki users  4952507568 Jul 20 07:37 stattmp5.bin
-rw------- 1 ravwoycicki users  2967488672 Jul 20 07:37 stattmp6.bin
-rw------- 1 ravwoycicki users  7597285408 Jul 20 07:37 stattmp7.bin
-rw------- 1 ravwoycicki users  8106177424 Jul 20 07:37 stattmp8.bin
-rw------- 1 ravwoycicki users  3929909488 Jul 20 07:37 stattmp9.bin
-rw------- 1 ravwoycicki users  4957729104 Jul 20 07:37 stattmpa.bin
-rw------- 1 ravwoycicki users  6613738832 Jul 20 07:37 stattmpb.bin
-rw------- 1 ravwoycicki users 10791303344 Jul 20 07:37 stattmpc.bin
-rw------- 1 ravwoycicki users  8101575248 Jul 20 07:37 stattmpd.bin
-rw------- 1 ravwoycicki users  8085920416 Jul 20 07:37 stattmpe.bin
-rw------- 1 ravwoycicki users 15860718176 Jul 20 07:37 stattmpf.bin
-rw------- 1 ravwoycicki users  1897812415 Jul 20 04:38
hybrid_int_skimmarknastyrepeats_nastyseq_preassembly2.0.lst
-rw------- 1 ravwoycicki users     2454361 Jul 19 14:18
hybrid_int_alignextends_preassembly1.0.txt
-rw------- 1 ravwoycicki users   294577845 Jul 19 13:22
miralog.ads_preassembly1.0.adsfacts.pclusters
-rw------- 1 ravwoycicki users  8555784505 Jul 19 12:29
miralog.ads_preassembly1.0.adsfacts
-rw------- 1 ravwoycicki users        2323 Jul 19 12:28
hybrid_int_vectorclip_pass.0.txt
-rw------- 1 ravwoycicki users  2130249792 Jul 19 12:28
miralog.ads_preassembly1.0.complement
-rw------- 1 ravwoycicki users   317608767 Jul 19 12:28
miralog.ads_preassembly1.0.reject
-rw------- 1 ravwoycicki users  2385529159 Jul 19 02:08
miralog.ads_preassembly1.0.forward
-rw------- 1 ravwoycicki users  2604708804 Jul 18 13:53
hybrid_int_posmatchc_preassembly.0.lst.reduced
-rw------- 1 ravwoycicki users  2889357325 Jul 18 13:49
hybrid_int_posmatchf_preassembly.0.lst.reduced
-rw------- 1 ravwoycicki users 17334675456 Jul 18 12:43
hybrid_int_normalisedskims_preassembly.0.bin
-rw------- 1 ravwoycicki users           0 Jul 18 11:25
hybrid_int_posmatch_multicopystat_preassembly.0.txt
-rw------- 1 ravwoycicki users  6285531902 Jul 18 11:23
hybrid_int_posmatchc_preassembly.0.lst
-rw------- 1 ravwoycicki users  6764936195 Jul 18 11:23
hybrid_int_posmatchf_preassembly.0.lst
-rw------- 1 ravwoycicki users        1219 Jul 18 11:23
hybrid_int_posmatch_megahubs_preassembly.0.lst
-rw------- 1 ravwoycicki users  1861993176 Jul 17 23:58
hybrid_int_skimmarknastyrepeats_nastyseq.0.lst
-rw------- 1 ravwoycicki users   379190990 Jul 16 16:10
hybrid_readpoolinfo.lst
-rw------- 1 ravwoycicki users           0 Jul 16 15:59
hybrid_error_reads_invalid


---------- Forwarded message ----------
From: Rafał Woycicki <rafalwoycicki@xxxxxxxxx>
Date: 2009/7/23
Subject: Asking about hybrid assembly
To: bach@xxxxxxxxxxxx


Dear Bastien,

I am doing hybrid assembly using MIRA 2.9.46x1 on the plant genome (~400
Mbp) with 8x unpaired 454 Titanium, 4x paired 454 Titanium (3kbp) and BAC
ends.

The program is working now for 1 week using at most 150 GB of RAM and
(sometimes) 10 cores on IA64.

I suppose that everythink is going right cause it is putting new files in
log directory, but my question is: Do you know how more long it could take
it to finish?

It was feeded with ~ 14 Millions Titanium reads and 65000 Sanger reads.

Thank you for any thoughts.

Best regards,
Rafal


-- 
---
Rafal Woycicki MSc
PhD Student
Dept. of Plant Genetics, Breeding and Biotechnology
Faculty of Horticulture and Landscape Architecture
Warsaw University of Life Sciences - SGGW
Warsaw/Poland



-- 
---
Rafal Woycicki MSc
PhD Student
Dept. of Plant Genetics, Breeding and Biotechnology
Faculty of Horticulture and Landscape Architecture
Warsaw University of Life Sciences - SGGW
Warsaw/Poland



-- 
---
Rafal Woycicki MSc
PhD Student
Dept. of Plant Genetics, Breeding and Biotechnology
Faculty of Horticulture and Landscape Architecture
Warsaw University of Life Sciences - SGGW
Warsaw/Poland

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