[mira_talk] mira not assembling

  • From: "Chauhan, Archana" <achauha1@xxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Fri, 13 Apr 2012 20:01:09 +0000

Attached please find the log file. I do not understand (i)The NFS system. How 
do I modify the assembly command to redirect the tmp directory somewhere else 
(ii)What is SSD (iii)Why is mira also using Sanger files/data when I am not 
assembling sander data? Thank you.


Regards
Archana
-----Original Message-----
From: Chauhan, Archana
Sent: Thursday, April 12, 2012 9:27 AM
To: 'mira_talk@xxxxxxxxxxxxx'
Subject: RE: mira_talk Digest V5 #65

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.

To (un-)subscribe the MIRA mailing lists, see:
        http://www.chevreux.org/mira_mailinglists.html

After subscribing, mail general questions to the MIRA talk mailing list:
        mira_talk@xxxxxxxxxxxxx

To report bugs or ask for features, please use the new ticketing system at:
        http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.


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&nbsp; log file .... check out ur files are properly extracted



From: "Chauhan, Archana" &lt;achauha1@xxxxxxx&gt;
Sent: Wed, 11 Apr 2012 23:41:21
To: "mira_talk@xxxxxxxxxxxxx" &lt;mira_talk@xxxxxxxxxxxxx&gt;
Subject: [mira_talk] mira  not assembling





 


Hi,
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; I am using mira for the first time.&nbsp; 
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 &gt;&amp;log_assembly &nbsp;

&nbsp;

[Newton:psi00a data]$ sff_extract -o HK44 ../origdata/FPBW0DM01.sff Working on 
'../origdata/FPBW0DM01.sff':
Converting '../origdata/FPBW0DM01.sff' ...&nbsp; 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 "&gt;" | 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
&gt;titlinker1
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG
&gt;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 ...&nbsp; ok.
Searching linker sequences with SSAHA2 (this may take a while) ...&nbsp; ok.
Parsing SSAHA2 result file ...&nbsp; done.
Converting '../origdata/GFW0S2V01.sff' ...&nbsp; done.
Converted 263887 reads into 481730 sequences.
[Newton:psi00a data]$ ls -l
total 1743865
-rw-r--r--+ 1 achauha1 users&nbsp; 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&nbsp; 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&nbsp; 420393768 Apr 11 13:59 
-rw-r--r--+ 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&nbsp; 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&nbsp; HK44_in.454.fasta.qual&nbsp; 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 -&gt; ../../data/HK44_in.454.fasta lrwxrwxrwx 1 
achauha1 users 33 Apr 11 14:04 HK44_in.454.fasta.qual -&gt; 
../../data/HK44_in.454.fasta.qual lrwxrwxrwx 1 achauha1 users 36 Apr 11 14:04 
HK44_traceinfo_in.454.xml -&gt; ../../data/HK44_traceinfo_in.454.xml
[Newton:psi00a arc_041112]$ mira --project=HK44 
--job=denovo,genome,accurate,454 &gt;&amp;log_assembly [Newton:psi00a 
arc_041112]$ mira --project=HK44 --job=denovo,genome,accurate,454 
&gt;&amp;log_assembly [Newton:psi00a arc_041112]$ ls HK44_assembly&nbsp; 
HK44_in.454.fasta&nbsp; HK44_in.454.fasta.qual&nbsp; 
HK44_traceinfo_in.454.xml&nbsp; 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]$

&nbsp;
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.
&nbsp;
I am not able to figure out what is going wrong. I wd appreciate if you could 
guide me.
&nbsp;
Regards,
Archie

 



------------------------------

End of mira_talk Digest V5 #65
******************************


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.

To (un-)subscribe the MIRA mailing lists, see:
        http://www.chevreux.org/mira_mailinglists.html

After subscribing, mail general questions to the MIRA talk mailing list:
        mira_talk@xxxxxxxxxxxxx

To report bugs or ask for features, please use the new ticketing system at:
        http://sourceforge.net/apps/trac/mira-assembler/
This ensures that requests don't get lost.


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
                                                       [454]  yes
            Template insert size minimum (tismin)   :  [san]  -1
                                                       [454]  -1
            Template insert size maximum (tismax)   :  [san]  -1
                                                       [454]  -1
            Template partner build direction (tpbd) :  [san]  -1
                                                       [454]  -1
        Colour reads by hash frequency (crhf)       : yes

  Load reads options (-LR):
        Load sequence data (lsd)                    :  [san]  no
                                                       [454]  yes
            File type (ft)                          :  [san]  fasta
                                                       [454]  fastq
            External quality (eq)                   : from SCF (scf)
                Ext. qual. override (eqo)           : no
                Discard reads on e.q. error (droeqe): no
            Solexa scores in qual file (ssiqf)      : no
            FASTQ qual offset (fqqo)                :  [san]  0
                                                       [454]  0

        Wants quality file (wqf)                    :  [san]  yes
                                                       [454]  yes

        Read naming scheme (rns)                    :  [san] Sanger Institute 
(sanger)
                                                       [454] forward/reverse 
(fr)

        Merge with XML trace info (mxti)            :  [san]  no
                                                       [454]  yes

        Filecheck only (fo)                         : no

  Assembly options (-AS):
        Number of passes (nop)                      : 5
            Skim each pass (sep)                    : yes
        Maximum number of RMB break loops (rbl)     : 3
        Maximum contigs per pass (mcpp)             : 0

        Minimum read length (mrl)                   :  [san]  80
                                                       [454]  40
        Minimum reads per contig (mrpc)             :  [san]  2
                                                       [454]  5
        Base default quality (bdq)                  :  [san]  10
                                                       [454]  10
        Enforce presence of qualities (epoq)        :  [san]  yes
                                                       [454]  yes

        Automatic repeat detection (ard)            : yes
            Coverage threshold (ardct)              :  [san]  2
                                                       [454]  2
            Minimum length (ardml)                  :  [san]  400
                                                       [454]  200
            Grace length (ardgl)                    :  [san]  40
                                                       [454]  20
            Use uniform read distribution (urd)     : no
              Start in pass (urdsip)                : 4
              Cutoff multiplier (urdcm)             :  [san]  1.5
                                                       [454]  1.5
        Keep long repeats separated (klrs)          : no

        Spoiler detection (sd)                      : yes
            Last pass only (sdlpo)                  : yes

        Use genomic pathfinder (ugpf)               : yes

        Use emergency search stop (uess)            : yes
            ESS partner depth (esspd)               : 500
        Use emergency blacklist (uebl)              : yes
        Use max. contig build time (umcbt)          : no
            Build time in seconds (bts)             : 10000

  Strain and backbone options (-SB):
        Load straindata (lsd)                       : no
        Assign default strain (ads)                 :  [san]  no
                                                       [454]  no
            Default strain name (dsn)               :  [san]  StrainX
                                                       [454]  StrainX
        Load backbone (lb)                          : no
            Start backbone usage in pass (sbuip)    : 3
            Backbone file type (bft)                : fasta
            Backbone base quality (bbq)             : 30
            Backbone strain name (bsn)              : ReferenceStrain
                Force for all (bsnffa)              : no
            Backbone rail from strain (brfs)        : 
            Backbone rail length (brl)              : 0
            Backbone rail overlap (bro)             : 0
            Also build new contigs (abnc)           : yes

  Dataprocessing options (-DP):
        Use read extensions (ure)                   :  [san]  yes
                                                       [454]  no
            Read extension window length (rewl)     :  [san]  30
                                                       [454]  15
            Read extension w. maxerrors (rewme)     :  [san]  2
                                                       [454]  2
            First extension in pass (feip)          :  [san]  0
                                                       [454]  0
            Last extension in pass (leip)           :  [san]  0
                                                       [454]  0

  Clipping options (-CL):
        Merge with SSAHA2/SMALT vector screen (msvs):  [san]  no
                                                       [454]  no
            Gap size (msvsgs)                       :  [san]  10
                                                       [454]  8
            Max front gap (msvsmfg)                 :  [san]  60
                                                       [454]  8
            Max end gap (msvsmeg)                   :  [san]  120
                                                       [454]  12
            Strict front clip (msvssfc)             :  [san]  0
                                                       [454]  0
            Strict end clip (msvssec)               :  [san]  0
                                                       [454]  0
        Possible vector leftover clip (pvlc)        :  [san]  yes
                                                       [454]  no
            maximum len allowed (pvcmla)            :  [san]  18
                                                       [454]  18
        Min qual. threshold for entire read (mqtfer):  [san]  0
                                                       [454]  0
            Number of bases (mqtfernob)             :  [san]  0
                                                       [454]  0
        Quality clip (qc)                           :  [san]  no
                                                       [454]  no
            Minimum quality (qcmq)                  :  [san]  20
                                                       [454]  20
            Window length (qcwl)                    :  [san]  30
                                                       [454]  30
        Bad stretch quality clip (bsqc)             :  [san]  yes
                                                       [454]  no
            Minimum quality (bsqcmq)                :  [san]  20
                                                       [454]  5
            Window length (bsqcwl)                  :  [san]  30
                                                       [454]  20
        Masked bases clip (mbc)                     :  [san]  yes
                                                       [454]  yes
            Gap size (mbcgs)                        :  [san]  20
                                                       [454]  5
            Max front gap (mbcmfg)                  :  [san]  40
                                                       [454]  12
            Max end gap (mbcmeg)                    :  [san]  60
                                                       [454]  12
        Lower case clip (lcc)                       :  [san]  no
                                                       [454]  yes
        Clip poly A/T at ends (cpat)                :  [san]  no
                                                       [454]  no
            Keep poly-a signal (cpkps)              :  [san]  no
                                                       [454]  no
            Minimum signal length (cpmsl)           :  [san]  12
                                                       [454]  12
            Max errors allowed (cpmea)              :  [san]  1
                                                       [454]  1
            Max gap from ends (cpmgfe)              :  [san]  9
                                                       [454]  9
        Clip 3 prime polybase (c3pp)                :  [san]  no
                                                       [454]  no
            Minimum signal length (c3ppmsl)         :  [san]  12
                                                       [454]  12
            Max errors allowed (c3ppmea)            :  [san]  2
                                                       [454]  2
            Max gap from ends (c3ppmgfe)            :  [san]  9
                                                       [454]  9
        Clip known adaptors right (ckar)            :  [san]  no
                                                       [454]  yes
        Ensure minimum left clip (emlc)             :  [san]  yes
                                                       [454]  no
            Minimum left clip req. (mlcr)           :  [san]  25
                                                       [454]  4
            Set minimum left clip to (smlc)         :  [san]  30
                                                       [454]  4
        Ensure minimum right clip (emrc)            :  [san]  no
                                                       [454]  no
            Minimum right clip req. (mrcr)          :  [san]  10
                                                       [454]  10
            Set minimum right clip to (smrc)        :  [san]  20
                                                       [454]  15

        Apply SKIM chimera detection clip (ascdc)   : yes
        Apply SKIM junk detection clip (asjdc)      : no

        Propose end clips (pec)                     : yes
            Bases per hash (pecbph)                 : 27
            Handle Solexa GGCxG problem (pechsgp)   : yes

        Clip bad solexa ends (cbse)                 : yes

  Parameters for SKIM algorithm (-SK):
        Number of threads (not)                     : 2

        Also compute reverse complements (acrc)     : yes
        Bases per hash (bph)                        : 21
        Hash save stepping (hss)                    : 1
        Percent required (pr)                       :  [san]  70
                                                       [454]  80

        Max hits per read (mhpr)                    : 2000
        Max megahub ratio (mmhr)                    : 0

        SW check on backbones (swcob)               : no

        Freq. est. min normal (fenn)                : 0.4
        Freq. est. max normal (fexn)                : 1.6
        Freq. est. repeat (fer)                     : 1.9
        Freq. est. heavy repeat (fehr)              : 8
        Freq. est. crazy (fecr)                     : 20
        Mask nasty repeats (mnr)                    : yes
            Nasty repeat ratio (nrr)                : 100
        Repeat level in info file (rliif)           : 6

        Max hashes in memory (mhim)                 : 15000000
        MemCap: hit reduction (mchr)                : 2048

  Pathfinder options (-PF):
        Use quick rule (uqr)                        :  [san]  yes
                                                       [454]  yes
            Quick rule min len 1 (qrml1)            :  [san]  200
                                                       [454]  80
            Quick rule min sim 1 (qrms1)            :  [san]  90
                                                       [454]  90
            Quick rule min len 2 (qrml2)            :  [san]  100
                                                       [454]  60
            Quick rule min sim 2 (qrms2)            :  [san]  95
                                                       [454]  95
        Backbone quick overlap min len (bqoml)      :  [san]  150
                                                       [454]  80
        Max. start cache fill time (mscft)          : 5

  Align parameters for Smith-Waterman align (-AL):
        Bandwidth in percent (bip)             :  [san]  20
                                                  [454]  20
        Bandwidth max (bmax)                   :  [san]  130
                                                  [454]  80
        Bandwidth min (bmin)                   :  [san]  25
                                                  [454]  20
        Minimum score (ms)                     :  [san]  30
                                                  [454]  15
        Minimum overlap (mo)                   :  [san]  17
                                                  [454]  20
        Minimum relative score in % (mrs)      :  [san]  70
                                                  [454]  70
        Solexa_hack_max_errors (shme)          :  [san]  0
                                                  [454]  0
        Extra gap penalty (egp)                :  [san]  no
                                                  [454]  yes
            extra gap penalty level (egpl)     :  [san] low
                                                  [454] reject_codongaps
            Max. egp in percent (megpp)        :  [san]  100
                                                  [454]  100

  Contig parameters (-CO):
        Name prefix (np)                                         : HK44
        Reject on drop in relative alignment score in % (rodirs) :  [san]  25
                                                                    [454]  30
        Mark repeats (mr)                                        : yes
            Only in result (mroir)                               : no
            Assume SNP instead of repeats (asir)                 : no
            Minimum reads per group needed for tagging (mrpg)    :  [san]  2
                                                                    [454]  4
            Minimum neighbour quality needed for tagging (mnq)   :  [san]  20
                                                                    [454]  20
            Minimum Group Quality needed for RMB Tagging (mgqrt) :  [san]  30
                                                                    [454]  25
            End-read Marking Exclusion Area in bases (emea)      :  [san]  1
                                                                    [454]  1
                Set to 1 on clipping PEC (emeas1clpec)           : yes
            Also mark gap bases (amgb)                           :  [san]  yes
                                                                    [454]  no
                Also mark gap bases - even multicolumn (amgbemc) :  [san]  yes
                                                                    [454]  yes
                Also mark gap bases - need both strands (amgbnbs):  [san]  yes
                                                                    [454]  yes
        Force non-IUPAC consensus per sequencing type (fnicpst)  :  [san]  no
                                                                    [454]  no
        Merge short reads (msr)                                  :  [san]  no
                                                                    [454]  no
            Keep ends unmerged (msrkeu)                          :  [san]  -1
                                                                    [454]  -1
        Gap override ratio (gor)                                 :  [san]  66
                                                                    [454]  66

  Edit options (-ED):
        Automatic contig editing (ace)              :  [san]  no
                                                       [454]  yes
     Sanger only:
        Strict editing mode (sem)                   : no
        Confirmation threshold in percent (ct)      : 50

  Misc (-MI):
        Stop on NFS (sonfs)                         : yes
        Extended log (el)                           : no
        Large contig size (lcs)                     : 500
        Large contig size for stats(lcs4s)          : 5000
        Stop on max read name length (somrnl)       : 40

  Directories (-DI):
        Working directory                 : 
        When loading EXP files            : 
        When loading SCF files            : 
        Top directory for writing files   : HK44_assembly
        For writing result files          : HK44_assembly/HK44_d_results
        For writing result info files     : HK44_assembly/HK44_d_info
        For writing tmp files             : HK44_assembly/HK44_d_tmp
        Tmp redirected to (trt)           : 
        For writing checkpoint files      : HK44_assembly/HK44_d_chkpt

  File names (-FN):
        When loading sequences from FASTA            :  [san]  
HK44_in.sanger.fasta
                                                        [454]  HK44_in.454.fasta
        When loading qualities from FASTA quality    :  [san]  
HK44_in.sanger.fasta.qual
                                                        [454]  
HK44_in.454.fasta.qual
        When loading sequences from FASTQ            :  [san]  
HK44_in.sanger.fastq
                                                        [454]  HK44_in.454.fastq
        When loading project from CAF                : HK44_in.sanger.caf
        When loading project from MAF (disabled)     : HK44_in.sanger.maf
        When loading EXP fofn                        : HK44_in.sanger.fofn
        When loading project from PHD                : HK44_in.phd.1
        When loading strain data                     : HK44_straindata_in.txt
        When loading XML trace info files            :  [san]  
HK44_traceinfo_in.sanger.xml
                                                        [454]  
HK44_traceinfo_in.454.xml
        When loading SSAHA2 vector screen results    : 
HK44_ssaha2vectorscreen_in.txt
        When loading SMALT vector screen results     : 
HK44_smaltvectorscreen_in.txt

        When loading backbone from MAF               : HK44_backbone_in.maf
        When loading backbone from CAF               : HK44_backbone_in.caf
        When loading backbone from GenBank           : HK44_backbone_in.gbf
        When loading backbone from GFF3              : HK44_backbone_in.gff3
        When loading backbone from FASTA             : HK44_backbone_in.fasta


  Output files (-OUTPUT/-OUT):
        Save simple singlets in project (sssip)      :  [san]  no
                                                        [454]  no
        Save tagged singlets in project (stsip)      :  [san]  yes
                                                        [454]  yes

        Remove rollover tmps (rrot)                  : yes
        Remove tmp directory (rtd)                   : no

    Result files:
        Saved as CAF                       (orc)     : yes
        Saved as MAF                       (orm)     : yes
        Saved as FASTA                     (orf)     : yes
        Saved as GAP4 (directed assembly)  (org)     : no
        Saved as phrap ACE                 (ora)     : yes
        Saved as GFF3                     (org3)     : no
        Saved as HTML                      (orh)     : no
        Saved as Transposed Contig Summary (ors)     : yes
        Saved as simple text format        (ort)     : no
        Saved as wiggle                    (orw)     : yes

    Temporary result files:
        Saved as CAF                       (otc)     : yes
        Saved as MAF                       (otm)     : no
        Saved as FASTA                     (otf)     : no
        Saved as GAP4 (directed assembly)  (otg)     : no
        Saved as phrap ACE                 (ota)     : no
        Saved as HTML                      (oth)     : no
        Saved as Transposed Contig Summary (ots)     : no
        Saved as simple text format        (ott)     : no

    Extended temporary result files:
        Saved as CAF                      (oetc)     : no
        Saved as FASTA                    (oetf)     : no
        Saved as GAP4 (directed assembly) (oetg)     : no
        Saved as phrap ACE                (oeta)     : no
        Saved as HTML                     (oeth)     : no
        Save also singlets               (oetas)     : no

    Alignment output customisation:
        TEXT characters per line (tcpl)              : 60
        HTML characters per line (hcpl)              : 60
        TEXT end gap fill character (tegfc)          :  
        HTML end gap fill character (hegfc)          :  

    File / directory output names:
        CAF             : HK44_out.caf
        MAF             : HK44_out.maf
        FASTA           : HK44_out.unpadded.fasta
        FASTA quality   : HK44_out.unpadded.fasta.qual
        FASTA (padded)  : HK44_out.padded.fasta
        FASTA qual.(pad): HK44_out.padded.fasta.qual
        GAP4 (directory): HK44_out.gap4da
        ACE             : HK44_out.ace
        HTML            : HK44_out.html
        Simple text     : HK44_out.txt
        TCS overview    : HK44_out.tcs
        Wiggle          : HK44_out.wig
------------------------------------------------------------------------------
Creating directory HK44_assembly ... done.
Creating directory HK44_assembly/HK44_d_tmp ... done.
Creating directory HK44_assembly/HK44_d_results ... done.
Creating directory HK44_assembly/HK44_d_info ... done.
Creating directory HK44_assembly/HK44_d_chkpt ... done.






WARNING WARNING WARNING!

It looks like the tmp directory is on a NFS (Network File System) mount. This
will slow down MIRA *considerably* ... by about a factor of 10!
If you don't want that, you have three possibilities:

1) RECOMMENDED! Use -DI:trt to redirect the tmp directory somewhere else on a
   local disk or even SSD.
2) POSSIBLE: put the whole project somewhere else and restart MIRA.
3) ABSOLUTELY NOT RECOMMENDED AT ALL: use "-MI:sonfs=no" to tell MIRA not
   to stop when it finds the tmp directory on NFS.

If you do not know what NFS is and which directory to use in "-DI:trt", ask
your local system administrator to guide you.


Fatal error (may be due to problems of the input data or parameters):

"Tmp directory is on a NFS mount ... but we don't want that."

->Thrown: void Assembly::checkForNFSMountOnTmpDir()
->Caught: main

Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.

Subscribing / unsubscribing to mira talk, see: 
//www.freelists.org/list/mira_talk

CWD: /data/achauha1/HK44/assembly/arc_041112
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.

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