[mira_talk] Re: [mira_talk] mira not assembling

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

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