[Himalaya]

Hi Francesco
Ya may be nobody is able to run ALLPATHS..
If anyone knows the error is post on 07-02-2010 plz post it.
Thank you

[francesco.vezzi]

Hi
at the end it seems that nobody is able to run ALLPATHS is that true?

F.

[corthay]

Hi Himalaya,

I got the error message when I've used Allpaths ver3.2 so I've used
ver 3-33800 for import my data. Unfortunately, I've not solved the
problem as it may be time-consuming to check the source code.

Thanks
Corthay.

Hi Corthay
Earlier I posted the error as you got. I couldn't find the solution of that. Hope you have solved it . Can you please tell me what was that?

Himalaya

[Himalaya]

Hi Corthay
Earlier I posted the error as you got. I couldn't find the solution of that. Hope you have solved it . Can you please tell me what was that?

Himalaya

[Himalaya]

Hi Corthay
I ran into the same problem that you posted on 06-01-2010. There is no any difference in that error and my error. Anyway i am posting my error as well.

Source directory is: /scratch/shresthr/sra_ncbi_ecoli
reading reads data from /scratch/shresthr/sra_ncbi_ecoli/frag_reads_lib_stats
FILE LIBRARY_NAME PAIRED JUMPING SEP DEV
ecolipairA library_1 T F 60 20
ecolipairB library_1 T F 60 20
Fri Jul 02 09:34:06 2010 Preparing data...
Fri Jul 02 09:34:06 2010 Found paired read files:
/scratch/shresthr/sra_ncbi_ecoli/ecolipairA
/scratch/shresthr/sra_ncbi_ecoli/ecolipairB
Fri Jul 02 09:34:06 2010 Loading reads
Fri Jul 02 09:34:56 2010 Loading quals
Fri Jul 02 09:35:51 2010 Filtering out noisy paired reads...
Before RemoveReads:7047668 7047668
After RemoveReads:7047264 7047264
Before RemoveReads:7047668 7047668
After RemoveReads:7047264 7047264
Fri Jul 02 09:35:52 2010 Removed 808 out of 14095336 reads
Fri Jul 02 09:35:52 2010 Writing reads
Fri Jul 02 09:36:13 2010 Writing quals
Fri Jul 02 09:36:34 2010 Building pairing information
Fri Jul 02 09:36:35 2010 Closing open files
Program PrepareAllPathsInput failed to make target $(DATA)/frag_reads_orig.pairs
/bin/sh: @echo: command not found
make: *** [/usr/users/tgac/shresthr/allpath_test//unknown/mydata/frag_reads_orig.fastb] Error 1
make: *** Deleting file `/usr/users/tgac/shresthr/allpath_test//unknown/mydata/frag_reads_orig.fastb'


Looks like the command PrepareAllPathsInput did not complete:
The following files are missing: 1
$(DATA)/frag_reads_orig.fastb
The following files are incomplete: 1
$(DATA)/frag_reads_orig.qualb
Cleaning up all targets of this command...
Moving $(DATA)/frag_reads_orig.qualb to $(DATA)/makeinfo/frag_reads_orig.qualb.incomplete

Fri Jul 02 09:36:55 2010 : Pipeline Finished. Run directory was
/usr/users/tgac/shresthr/allpath_test//unknown/mydata/mytestrun


*** Make encountered an error, see above for error messages. ***

I thought everything was fine and it's importing the reads. Suddenly i got this problem. Hope you have sort out this problem as well. What might be wrong here?

Himalaya

[Himalaya]

Hi Himalaya,

You can use only following values for K-mer, as I've roughly checked the source code.
12,20,26,40,64,80,88,96

The "Metric "SEP" is undefined" error is occured when you do not prepare
"frag_reads_lib_stats" or "jump_reads_lib_stats" in the SOURCE_DIR.
Here is my sample files.

::::::::::::::
frag_reads_lib_stats
::::::::::::::
FILE LIBRARY_NAME PAIRED JUMPING SEP DEV
ecolisim.180.A.fasta Solexa180 T F 180 18
ecolisim.180.B.fasta Solexa180 T F 180 18

::::::::::::::
jump_reads_lib_stats
::::::::::::::
FILE LIBRARY_NAME PAIRED JUMPING SEP DEV
ecolisim.3000.compl.A.fasta Solexa3000 T T 3000 300
ecolisim.3000.compl.B.fasta Solexa3000 T T 3000 300

::::::::::::::
ploidy
::::::::::::::
1

Good Luck !
Corthay

hi Corthay
Thanks a lot.
Now it works. I am able to import the reads. Thanks for being so helpful.

Himalaya

[corthay]

Hi Himalaya,

You can use only following values for K-mer, as I've roughly checked the source code.
12,20,26,40,64,80,88,96

The "Metric "SEP" is undefined" error is occured when you do not prepare
"frag_reads_lib_stats" or "jump_reads_lib_stats" in the SOURCE_DIR.
Here is my sample files.

::::::::::::::
frag_reads_lib_stats
::::::::::::::
FILE LIBRARY_NAME PAIRED JUMPING SEP DEV
ecolisim.180.A.fasta Solexa180 T F 180 18
ecolisim.180.B.fasta Solexa180 T F 180 18

::::::::::::::
jump_reads_lib_stats
::::::::::::::
FILE LIBRARY_NAME PAIRED JUMPING SEP DEV
ecolisim.3000.compl.A.fasta Solexa3000 T T 3000 300
ecolisim.3000.compl.B.fasta Solexa3000 T T 3000 300

::::::::::::::
ploidy
::::::::::::::
1

Good Luck !
Corthay

[Himalaya]

Hi Corthay again
I tried some more options and got different errors now
Well there was not much different command than the one i posted. I only change the lowercase k to uppercase K and gave the value 31. The error generated was

Not implemented for K=31.
This makes sense as my reads length were 100 bp.
so i changed K=96 and this time the error message has following:
Metric "SEP" is undefined.
...
...
...
Looks like the command PrepareAllPathsInput did not complete:
The following files are missing: 1
$(DATA)/frag_reads_orig.fastb
The following files are incomplete: 1
$(DATA)/frag_reads_orig.qualb
Cleaning up all targets of this command...

Do we have to prepare the file frag_reads_lib_stat file that was specified in manual, which has five values: file library_name paired jumping sep dev
and put that file in the SOURCE_DIR.

Waiting for the reply
Thanks
Himalaya

[Himalaya]

Hi Corthay
Thanks a lot for reply.
seems like my command is not different than yours while importing. The only difference is that you have given the value of k while importing but when i give the value of k, it gives error saying -

You should not have specified a value for k.
To see the syntax for this command, type "RunAllPaths3G -h".

Did you get this error?
And this you get the error saying "frag_reads_orig.fastb" is missing. if this file is created during import then in my case this file is not created. Any idea what might be wrong.

Thanks again.

[corthay]

Hi Himalaya,

The file "frag_reads_orig.fastb" is a binary sequence
file as input for allpaths. It's generated in import step.

I've used following command for import and standard.
----- import -----
RunAllPaths3G \
PRE=assembly \
DATA_SUBDIR=MyData \
RUN=MyRun \
REFERENCE_NAME=Ecoli \
TARGETS=import \
SOURCE_DIR=simrd \
K=96 \
OVERWRITE=True
-------------------
---- standard -----
RunAllPaths3G \
PRE=assembly \
DATA_SUBDIR=MyData \
RUN=MyRun \
REFERENCE_NAME=Ecoli \
TARGETS=standard \
K=96 \
OVERWRITE=True
-------------------

Thanks.
Corthay

[Himalaya]

Hi Corthay
I downloaded allpaths3-33685 and i am also trying to import only.
But there is error. In the error there is following messge

Looks like the command PrepareAllPathsInput did not complete:
The following files are missing: 1
$(DATA)/frag_reads_orig.fastb
The following files are incomplete: 1
$(DATA)/frag_reads_orig.qualb
Cleaning up all targets of this command...

What is this file "frag_reads_orig.fastb" and its quala file.
I have paired end files, pair.a.fasta and pair.b.fasta and their files pair.a.quala and pair.b.quala. Lets assume these all files are in folder "unknown" in my home directory.
Then my command was
RunAllPaths3G PRE=$HOME/allpaths_test DATA_SUBDIR=mytestdata RUN=mytestrun EVALUATION=NONE REFERENCE_NAME=Unknown TARGETS=import SOURCE_DIR=~/unknown_sp/ OVERWRITE=True
This command gave the above error.
Please help me. Can you please provide me your sample command for "TARGET=IMPORT" and "TARGET=STANDARD"

Thanks a lot for the help
Himalaya

[corthay]

Hi Himalaya,

I've used ver. 3-33800 for import as ver 3.2 have not worked and
I've used ver. 3.2 (stable version) for standard as ver 3-33800 have not worked.
You can get latest source code from following site.
ftp://ftp.broadinstitute.org/pub/crd...t_source_code/

Apparently, it's successful but I am still checking the result.
For your information, I've prepared E.coli simulated reads as following.
- insert length : 180bp +/- 18bp, read length : 110bp, 45x (fragment)
- insert length : 3000bp +/- 300bp, read length : 110bp, 45x (jumping)

Hope that this is of some use to you.

Thanks
Corthay

[Himalaya]

Hi
I am new in allpaths as well.
I am also now having the same problem as Corthay
Hi Corthay, if you have solved the problem, please post it.
Thank you

[francesco.vezzi]

Hi
I spend one week trying to install ALLPATHS without results. It seems that the source code is designed to be compiled only on the machines of the authors... I never heard somebody that was able to install this assembler

My suggestion... don't loose time and use one between SOAPdenovo or ABySS

F.

[corthay]

Hi,

I have similar problem with allpaths. I've compiled Allpath ver3.2
with following command.

%autoconf
%./configure CC=gcc44 CXX=g++44
%make

It looks successesful but I got following error when I have tried to import
the sample S.pombe data.
(ftp://ftp.broadinstitute.org/pub/crd...S/Release-2-0/ )
-------------------------------------------------------------------------


Tue Jun 01 18:58:26 2010 Removed 866 out of 10636466 reads
Tue Jun 01 18:58:26 2010 Writing reads
Tue Jun 01 18:58:38 2010 Writing quals
Tue Jun 01 18:58:51 2010 Building pairing information
Tue Jun 01 18:58:53 2010 Closing open files
Program PrepareAllPathsInput failed to make target $(DATA)/frag_reads_orig.pairs
/bin/sh: @echo: command not found
make: *** [assembly/Spombe/MyData/frag_reads_orig.fastb] Error 1
make: *** Deleting file `assembly/Spombe/MyData/frag_reads_orig.fastb'


Looks like the command PrepareAllPathsInput did not complete:
The following files are missing: 1
$(DATA)/frag_reads_orig.fastb
The following files are incomplete: 1
$(DATA)/frag_reads_orig.qualb
Cleaning up all targets of this command...
Moving $(DATA)/frag_reads_orig.qualb to $(DATA)/makeinfo/frag_reads_orig.qualb.incomplete

Tue Jun 01 18:59:12 2010 : Pipeline Finished. Run directory was
assembly/Spombe/MyData/MyRun

*** Make encountered an error, see above for error messages. ***
-------------------------------------------------------------------------

Is there anyone who had the same problem before ?

Thanks,
Corthay