[mira_talk] Re: mira_talk Digest V5 #65
- From: "Chauhan, Archana" <achauha1@xxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 12 Apr 2012 13:27:16 +0000
Hi Chevreux,
The details of the los _assembly files are as under:
*******************************************************************************
[Newton:psi00b HK44_assembly]$ vi log_assembly
This is MIRA V3.4.0 (production version).
Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
Assembly Using Trace Signals and Additional Sequence Information.
Computer Science and Biology: Proceedings of the German Conference on
Bioinformatics (GCB) 99, pp. 45-56.
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Compiled by: bach
Sun Aug 21 17:50:30 CEST 2011
On: Linux arcadia 2.6.38-11-generic #48-Ubuntu SMP Fri Jul 29 19:02:55 UTC 2011
x86_64 x86_64 x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime settings (sorry, for debug):
Size of size_t : 8
Size of uint32 : 4
Size of uint32_t: 4
Size of uint64 : 8
Size of uint64_t: 8
Current system: Linux psi00a 2.6.18-194.17.1.el5 #1 SMP Wed Sep 29 12:09:22 EDT
2010 x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: --project=HK44 --job=denovo,genome,accurate,454
Parameters parsed without error, perfect.
-CL:pec and -CO:emeas1clpec are set, setting -CO:emea values to 1.
------------------------------------------------------------------------------
Parameter settings seen for:
Sanger data (also common parameters), 454 data
Used parameter settings:
General (-GE):
Project name in (proin) : HK44
Project name out (proout) : HK44
Number of threads (not) : 2
Automatic memory management (amm) : yes
Keep percent memory free (kpmf) : 15
Max. process size (mps) : 0
EST SNP pipeline step (esps) : 0
Use template information (uti) : [san] yes
"log_assembly" 486L, 22794C
**********************************************************************************************************************
Regards,
Archie
-----Original Message-----
From: FreeLists Mailing List Manager [mailto:ecartis@xxxxxxxxxxxxx]
Sent: Thursday, April 12, 2012 1:14 AM
To: mira_talk digest users
Subject: mira_talk Digest V5 #65
mira_talk Digest Wed, 11 Apr 2012 Volume: 05 Issue: 065
In This Issue:
[mira_talk] mira not assembling
[mira_talk] Re: mira not assembling
[mira_talk] =?utf-8?B?UmU6IFttaXJhX3RhbGtdIG1pcmEgIG5vdCBhc3
----------------------------------------------------------------------
From: "Chauhan, Archana" <achauha1@xxxxxxx>
Subject: [mira_talk] mira not assembling
Date: Wed, 11 Apr 2012 18:10:35 +0000
Hi,
I am using mira for the first time. I am trying to assemble my 454
unpaired and paired end reads with mira. I could successfully extracted the
both the unpaired and the paired end data from respective . sff files. Now I am
trying to run the assembly with following command:
mira --project=HK44 --jobÞnovo,genome,454 >&log_assembly
[Newton:psi00a data]$ sff_extract -o HK44 ../origdata/FPBW0DM01.sff Working on
'../origdata/FPBW0DM01.sff':
Converting '../origdata/FPBW0DM01.sff' ... done.
Converted 617042 reads into 617042 sequences.
[Newton:psi00a data]$ ls -l
total 1108371
-rw-r--r--+ 1 achauha1 users 326954919 Apr 11 13:51 HK44.fasta
-rw-r--r--+ 1 achauha1 users 957040435 Apr 11 13:51 HK44.fasta.qual
-rw-r--r--+ 1 achauha1 users 103997244 Apr 11 13:51 HK44.xml
[Newton:psi00a data]$ head -40 HK44.fasta | grep -v ">" | cut -c 1-30
tcagTGCCAGTGCTCGACCGAAGCGTCTGT tcagGTTGACTATTGAGTCGCCACCTGCGC
tcagTGTCGAAATTGACCCCGGAACACACT tcagCGCTGCGCTTGGCAACTTGAGCGCTT
tcagTTGCAGGGATCGCCCATGAAGCGCTT tcagCGCAGTAGATTGCGAGCATCAAGCAC
tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagAGATGACTGCCATTCCTACCGCGACC
tcagAATCCAGGTTCTTCGAATGGCAGAAT tcagTGCCTTGTTCTGCTCGATGCGGTTCT
tcagTCGCCATGCTCATGCAATGCCGCGTC tcagGACCTTGGCATCCAGCGCGCCAAGGT
tcagTGCCTTGTTCTGCTCGATGCGGTTCT tcagTTCAGGCCGAATCGAAGCATTGGGAC
tcagGTCTTGGCGCCGTGCTTGCCGATGTG tcagCTGGTAGAGAAGCACGTGCCAAGGCA
tcagTTCAGATCCGCTGGCGACAGCGGTCC tcagAAGTCCGGCTCCATCAGCAGCAGGCC
tcagCGTCGCGCATCGCTGCAACGTTATCT tcagTTTTTATCGCTTTCGGTCAACGTAAA [Newton:psi00a
data]$ cat ../origdata/linker.fasta
>titlinker1
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
>titlinker2
CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
[Newton:psi00a data]$ sff_extract -o HK44 -a -l ../origdata/linker.fasta -i
"insert_size:3000,insert_stdev:900" ../origdata/GFW0S2V01.sff Working on
'../origdata/GFW0S2V01.sff':
Creating temporary sequences from reads in '../origdata/GFW0S2V01.sff' ...
insert_size:3000,insert_stdev:900" ./origdata/GFW0S2V01.sff done.
Testing whether SSAHA2 is installed and can be launched ... ok.
Searching linker sequences with SSAHA2 (this may take a while) ... ok.
Parsing SSAHA2 result file ... done.
Converting '../origdata/GFW0S2V01.sff' ... done.
Converted 263887 reads into 481730 sequences.
[Newton:psi00a data]$ ls -l
total 1743865
-rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44.fasta
-rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 HK44.fasta.qual
-rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 HK44.xml
[Newton:psi00a data]$ mv HK44.fasta HK44_in.454.fasta [Newton:psi00a data]$ mv
HK44.fasta.qual HK44_in.454.fasta.qual [Newton:psi00a data]$ mv HK44.xml
HK44_traceinfo_in.454.xml [Newton:psi00a data]$ ls -l total 1834191
-rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44_in.454.fasta
-rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59
-rw-r--r--+ HK44_in.454.fasta.qual
-rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59
-rw-r--r--+ HK44_traceinfo_in.454.xml
[Newton:psi00a data]$ cd ../assembly/
[Newton:psi00a assembly]$ mkdir
[Newton:psi00a assembly]$ mkdir arc_041112 [Newton:psi00a assembly]$ ls
arc_041112
[Newton:psi00a assembly]$ cd arc_041112/ [Newton:psi00a arc_041112]$ ln -s
../../data/* .
[Newton:psi00a arc_041112]$ ls
HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml
[Newton:psi00a arc_041112]$ ls -l total 2 lrwxrwxrwx 1 achauha1 users 28 Apr 11
14:04 HK44_in.454.fasta -> ../../data/HK44_in.454.fasta lrwxrwxrwx 1 achauha1
users 33 Apr 11 14:04 HK44_in.454.fasta.qual ->
../../data/HK44_in.454.fasta.qual lrwxrwxrwx 1 achauha1 users 36 Apr 11 14:04
HK44_traceinfo_in.454.xml -> ../../data/HK44_traceinfo_in.454.xml
[Newton:psi00a arc_041112]$ mira --project=HK44 --jobÞnovo,genome,accurate,454
>&log_assembly [Newton:psi00a arc_041112]$ mira --project=HK44
--jobÞnovo,genome,accurate,454 >&log_assembly [Newton:psi00a arc_041112]$ ls
HK44_assembly HK44_in.454.fasta HK44_in.454.fasta.qual
HK44_traceinfo_in.454.xml log_assembly [Newton:psi00a arc_041112]$ cd
HK44_assembly/ [Newton:psi00a HK44_assembly]$ ls -l total 8
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_chkpt
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_info
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_results
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_tmp
[Newton:psi00a HK44_assembly]$ cd HK44_d_results/ [Newton:psi00a
HK44_d_results]$ ls [Newton:psi00a HK44_d_results]$ ls -l total 0
[Newton:psi00a HK44_d_results]$
The assembly command creates following subdirectories in the directory
"arc_04/11_12" but all are empty. It appears that mira is not assembling (as
the command finishes in 2-3 sec only) but does not give any errors either.
I am not able to figure out what is going wrong. I wd appreciate if you could
guide me.
Regards,
Archie
------------------------------
From: Bastien Chevreux <bach@xxxxxxxxxxxx>
Subject: [mira_talk] Re: mira not assembling
Date: Wed, 11 Apr 2012 20:37:55 +0200
On Apr 11, 2012, at 20:10 , Chauhan, Archana wrote:
> The assembly command creates following subdirectories in the directory
> “arc_04/11_12” but all are empty. It appears that mira is not assembling (as
> the command finishes in 2-3 sec only) but does not give any errors either.
>
> I am not able to figure out what is going wrong. I wd appreciate if you could
> guide me.
At first glance things should be working. Can you please post "log_assembly"
for me to have a look at?
B.
------------------------------
Date: 12 Apr 2012 04:28:12 -0000
Subject: [mira_talk] =?utf-8?B?UmU6IFttaXJhX3RhbGtdIG1pcmEgIG5vdCBhc3NlbWJsaW5n
From: "Abhishek sharma" <abhishek_btbin@xxxxxxxxxxxxxx>
send ur log file .... check out ur files are properly extracted
From: "Chauhan, Archana" <achauha1@xxxxxxx>
Sent: Wed, 11 Apr 2012 23:41:21
To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
Subject: [mira_talk] mira not assembling
Hi,
I am using mira for the first time.
I am trying to assemble my 454 unpaired and paired end reads with mira. I could
successfully extracted the both the unpaired and the paired end data from
respective . sff files. Now I am trying
to run the assembly with following command:
mira --project=HK44 --job=denovo,genome,454 >&log_assembly
[Newton:psi00a data]$ sff_extract -o HK44 ../origdata/FPBW0DM01.sff
Working on '../origdata/FPBW0DM01.sff':
Converting '../origdata/FPBW0DM01.sff' ... done.
Converted 617042 reads into 617042 sequences.
[Newton:psi00a data]$ ls -l
total 1108371
-rw-r--r--+ 1 achauha1 users 326954919 Apr 11 13:51 HK44.fasta
-rw-r--r--+ 1 achauha1 users 957040435 Apr 11 13:51 HK44.fasta.qual
-rw-r--r--+ 1 achauha1 users 103997244 Apr 11 13:51 HK44.xml
[Newton:psi00a data]$ head -40 HK44.fasta | grep -v ">" | cut -c 1-30
tcagTGCCAGTGCTCGACCGAAGCGTCTGT
tcagGTTGACTATTGAGTCGCCACCTGCGC
tcagTGTCGAAATTGACCCCGGAACACACT
tcagCGCTGCGCTTGGCAACTTGAGCGCTT
tcagTTGCAGGGATCGCCCATGAAGCGCTT
tcagCGCAGTAGATTGCGAGCATCAAGCAC
tcagTGCCTTGTTCTGCTCGATGCGGTTCT
tcagAGATGACTGCCATTCCTACCGCGACC
tcagAATCCAGGTTCTTCGAATGGCAGAAT
tcagTGCCTTGTTCTGCTCGATGCGGTTCT
tcagTCGCCATGCTCATGCAATGCCGCGTC
tcagGACCTTGGCATCCAGCGCGCCAAGGT
tcagTGCCTTGTTCTGCTCGATGCGGTTCT
tcagTTCAGGCCGAATCGAAGCATTGGGAC
tcagGTCTTGGCGCCGTGCTTGCCGATGTG
tcagCTGGTAGAGAAGCACGTGCCAAGGCA
tcagTTCAGATCCGCTGGCGACAGCGGTCC
tcagAAGTCCGGCTCCATCAGCAGCAGGCC
tcagCGTCGCGCATCGCTGCAACGTTATCT
tcagTTTTTATCGCTTTCGGTCAACGTAAA
[Newton:psi00a data]$ cat ../origdata/linker.fasta
>titlinker1
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
>titlinker2
CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA
[Newton:psi00a data]$ sff_extract -o HK44 -a -l ../origdata/linker.fasta -i
"insert_size:3000,insert_stdev:900" ../origdata/GFW0S2V01.sff
Working on '../origdata/GFW0S2V01.sff':
Creating temporary sequences from reads in '../origdata/GFW0S2V01.sff' ...
insert_size:3000,insert_stdev:900" ./origdata/GFW0S2V01.sff done.
Testing whether SSAHA2 is installed and can be launched ... ok.
Searching linker sequences with SSAHA2 (this may take a while) ... ok.
Parsing SSAHA2 result file ... done.
Converting '../origdata/GFW0S2V01.sff' ... done.
Converted 263887 reads into 481730 sequences.
[Newton:psi00a data]$ ls -l
total 1743865
-rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44.fasta
-rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 HK44.fasta.qual
-rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59 HK44.xml
[Newton:psi00a data]$ mv HK44.fasta HK44_in.454.fasta
[Newton:psi00a data]$ mv HK44.fasta.qual HK44_in.454.fasta.qual
[Newton:psi00a data]$ mv HK44.xml HK44_traceinfo_in.454.xml
[Newton:psi00a data]$ ls -l
total 1834191
-rw-r--r--+ 1 achauha1 users 420393768 Apr 11 13:59 HK44_in.454.fasta
-rw-r--r--+ 1 achauha1 users 1216785437 Apr 11 13:59 HK44_in.454.fasta.qual
-rw-r--r--+ 1 achauha1 users 241659226 Apr 11 13:59
HK44_traceinfo_in.454.xml
[Newton:psi00a data]$ cd ../assembly/
[Newton:psi00a assembly]$ mkdir
[Newton:psi00a assembly]$ mkdir arc_041112
[Newton:psi00a assembly]$ ls
arc_041112
[Newton:psi00a assembly]$ cd arc_041112/
[Newton:psi00a arc_041112]$ ln -s ../../data/* .
[Newton:psi00a arc_041112]$ ls
HK44_in.454.fasta HK44_in.454.fasta.qual HK44_traceinfo_in.454.xml
[Newton:psi00a arc_041112]$ ls -l
total 2
lrwxrwxrwx 1 achauha1 users 28 Apr 11 14:04 HK44_in.454.fasta ->
../../data/HK44_in.454.fasta
lrwxrwxrwx 1 achauha1 users 33 Apr 11 14:04 HK44_in.454.fasta.qual ->
../../data/HK44_in.454.fasta.qual
lrwxrwxrwx 1 achauha1 users 36 Apr 11 14:04 HK44_traceinfo_in.454.xml ->
../../data/HK44_traceinfo_in.454.xml
[Newton:psi00a arc_041112]$ mira --project=HK44
--job=denovo,genome,accurate,454 >&log_assembly
[Newton:psi00a arc_041112]$ mira --project=HK44
--job=denovo,genome,accurate,454 >&log_assembly
[Newton:psi00a arc_041112]$ ls
HK44_assembly HK44_in.454.fasta HK44_in.454.fasta.qual
HK44_traceinfo_in.454.xml log_assembly
[Newton:psi00a arc_041112]$ cd HK44_assembly/
[Newton:psi00a HK44_assembly]$ ls -l
total 8
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_chkpt
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_info
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_results
drwxr-xr-x+ 2 achauha1 users 2 Apr 11 14:06 HK44_d_tmp
[Newton:psi00a HK44_assembly]$ cd HK44_d_results/
[Newton:psi00a HK44_d_results]$ ls
[Newton:psi00a HK44_d_results]$ ls -l
total 0
[Newton:psi00a HK44_d_results]$
The assembly command creates following subdirectories in the directory
“arc_04/11_12†but all are empty. It appears that mira is not assembling
(as the command finishes in 2-3 sec only) but does not give any errors either.
I am not able to figure out what is going wrong. I wd appreciate if you could
guide me.
Regards,
Archie
------------------------------
End of mira_talk Digest V5 #65
******************************
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