[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

[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 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

[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

[francesco.vezzi]

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

F.

[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

[sundarsukumar]

Getting error in allpaths2.2

HI all, Please help me on this.

I am running allpaths 2.2 , actually i was trying 2 install allpaths 3.2 .,while i was trying to install, i couldn't able to install boost library proprely..

Here is my error

sundar@sundar-desktop:/media/ubuntu/Allpaths/allpaths-2.2/src$ ulimit -s 100000

sundar@sundar-desktop:/media/ubuntu/Allpaths/allpaths-2.2/src$ ./RunAllPaths PRE=input/ DATA_SUBDIR=MyTestData RUN=MyRun REFERENCE_NAME=Ecoli TARGETS=import SOURCE_DIR=input/input_source REFERENCE_FASTB=input/input.reference/genome.fastb K=20 EVALUATION=REFERENCE MAXPAR=1 PARALLEL_BATCHES=1

--------------------------------------------------------------------------------
Mon Aug 02 10:26:27 2010 run (pid=4467)
RunAllPaths PRE=input/ DATA_SUBDIR=MyTestData RUN=MyRun REFERENCE_NAME=Ecoli \
TARGETS=import SOURCE_DIR=input/input_source \
REFERENCE_FASTB=input/input.reference/genome.fastb K=20 \
EVALUATION=REFERENCE MAXPAR=1 PARALLEL_BATCHES=1
--------------------------------------------------------------------------------

running on sundar-desktop

MARK_TRUSTED_A_MIN_SUPPORT = 4, MARK_TRUSTED_A_MAX_UNSUPPORTED_TO_TEST = 5, MARK_TRUSTED_B_MIN_SUPPORT = 4, MARK_TRUSTED_B_MAX_UNSUPPORTED_TO_TEST = 5
run dir is
input//Ecoli/MyTestData/MyRun

Found existing genome.fastb file in reference directory.
Ignoring REFERENCE_FASTB option.
targetsToMake = 1
input//Ecoli/MyTestData/reads_orig.fastb

forceTargets = 0



Copy of makefile in: input//Ecoli/make_mgr/MyTestData/MyRun/test/2010-08-02T10:26:27.make
[PAPI]
[PAPI] === Getting data from the source directory into ALLPATHS format ===
[PAPI]
[PAPI] Calling PrepareAllPathsInput to create 11 file(s):
[PAPI]
[PAPI] $(DATA)/ploidy
[PAPI] $(DATA)/reads_orig.fastb
[PAPI] $(DATA)/reads_orig.lane_index
[PAPI] $(DATA)/reads_orig.lane_infos
[PAPI] $(DATA)/reads_orig.lanes
[PAPI] $(DATA)/reads_orig.lengths
[PAPI] $(DATA)/reads_orig.pairto
[PAPI] $(DATA)/reads_orig.pairto_index
[PAPI] $(DATA)/reads_orig.pairtob
[PAPI] $(DATA)/reads_orig.props
[PAPI] $(DATA)/reads_orig.qualb
[PAPI]
[PAPI] from 0 file(s):
[PAPI]
[PAPI]
[PAPI] PrepareAllPathsInput SOURCE_DIR=$(SOURCE) DATA_DIR=$(DATA) READS_OUT="reads_orig" STATS_IN=expected_lib_stats
/bin/sh: PrepareAllPathsInput: not found
make: *** [input//Ecoli/MyTestData/ploidy] Error 127


Mon Aug 02 10:26:28 2010: make finished, run dir was
input//Ecoli/MyTestData/MyRun


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

[pengchy]

"may be nobody is able to run ALLPATHS.."
Really?
We also have this question. Could anybody can help us?

[fishinabarrel]

I have been trying Allpaths-LG for a few days now. I got it to compile after dealing with an memory stack trace error (needed to set limit to 100000, rather than the setting of unlimited).

The programs run, but they fail to actually succeed. I get crashes at various stages of their perl scripts. I am posting this just as a word of caution to anyone else out there who might be thinking of using ALLPATHS-LG. Don't waste your time on this until there is some additional evidence that their software can be used universally.

[acopeland]

I won't make any claim about allpaths-lg being universally runnable, but I can say that we have been using it quite successfully on microbial and fungal projects.

To get workable binaries you will need gcc-4.3.2 or newer and boost-1.38 or newer (building these can be a bear). I can post configure commands if that's useful to anyone.

Finally, I strongly encourage anyone testing allpaths-lg to download the test data supplied by the Broad (ftp://ftp.broadinstitute.org/pub/crd....genome.tar.gz) and get this working before running your own data.

[corthay]

Hi all,

Finally, allpaths-lg works on my machine.

My OS is CentOS 5.3 and the version of allpaths-lg is 38003.

I would like to recommend retrying allpaths-lg as it's getting familiar.

[fishinabarrel]

Hi all,

Finally, allpaths-lg works on my machine.

My OS is CentOS 5.3 and the version of allpaths-ls is 38003.

I would like to recommend retrying allpaths-lg as it's getting familiar.

Thank you Corthay !
I have not retried this tool since about version 36861.

I will give it a go again and see how far I get.

[[email protected]]

Which De novo assembler?

We have human paired-end data from complete genomics. The read length is 70bp.Which is am appropriate software tool to use? I have come accross, SOPA denovo, allpaths-lg, Velvet and Abyss. Which of these is suitable for use on human data if a HPC environment is available?

[Himalaya]

We have human paired-end data from complete genomics. The read length is 70bp.Which is am appropriate software tool to use? I have come accross, SOPA denovo, allpaths-lg, Velvet and Abyss. Which of these is suitable for use on human data if a HPC environment is available?

I did a small comparative study of soap denovo, velvet, ABYSS and cortex. I could not use allpaths. SOAP devono is fast than other but uses very huge memory. ABYSS does better assembly but velvet is not bad as well. If I were you, I would use ABYSS and velvet both.

[[email protected]]

Abyss vs Velvet

I tried using the velvet formula for my RAM calculation and about 500 Gb is the answer for human sized genomes. Is that your experience too? Aslo, how many days approx. would it take? The HPC environment here has a max walltime of 96hrs.

Another question is regarding trimming, did you use any specific software or wrote your own scripts?