[mira_talk] Fwd: Asking about hybrid assembly
- From: Rafał Woycicki <rafalwoycicki@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 24 Jul 2009 17:04:32 +0200
---------- 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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