(Please use the list)
Hello,
I think I found the problem.
Can you try with the enclosed patch ?
To build Ray v2.2.0 with this patch:
wget http://sourceforge.net/projects/denovoassembler/files/Ray-v2.2.0.tar.bz2
wget
https://raw.github.com/sebhtml/patches/master/ray/Ray-v2.2.0-fix-for-amos-and-long-reads.patch
tar -xjf Ray-v2.2.0.tar.bz2
cd Ray-v2.2.0
patch -p1 < ../Ray-v2.2.0-fix-for-amos-and-long-reads.patch
make -j 20
mkdir -p ~/software/ray/2.2.0-1-long-reads-amos
cp Ray~/software/ray/2.2.0-1-long-reads-amos
-Sébastien
On 27/08/13 03:58 AM, Hornung, Bastian wrote:
Okay, that's then obviously not the problem.
I've for testing purposes installed a version locally, once with different
parameters, afterwards with the standard parameters, and loaded the PacBio data
into it. And it runs.
If I now try it again on our server (both the local linux machine as well as
the server are Ubuntu 12.04), no matter if I freshly compile it or use the
already present installation (also without any different installation
parameters) I get again a stack overflow warning, see the command line output:
Rank 0 is fetching file
/home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with lazy
loading (please wait...)
Rank 3 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 2 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 1 is fetching file
/home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with lazy
loading (please wait...)
Rank 4 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with lazy
loading (please wait...)
Rank 4: File /home/bastian/data/RAW/PacBio/all_ccs.fastq (Number 4) has 3699
sequences
Rank 2: File
/home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq (Number
2) has 9886736 sequences
Rank 3: File
/home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq (Number
3) has 9886736 sequences
Rank 0: File
/home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq (Number
0) has 34807392 sequences
Rank 1: File
/home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq (Number
1) has 34807392 sequences
Rank 0 wrote
/home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/NumberOfSequences.txt
Rank 0 wrote
/home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/SequencePartition.txt
***
Step: Counting sequences to assemble
Date: Tue Aug 27 09:42:39 2013
Elapsed time: 18 seconds
Since beginning: 18 seconds
***
Rank 0 is adding sequences to
/home/bastian/data/RAW/test_illumina_untrimmed_matepair_pacbio_ray_k31/AMOS.afg
Rank 0 is fetching file
/home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test_illumina_read_1/NG-5257_test_read_1.fastq with lazy
loading (please wait...)
adRank 0 is fetching file
/home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test_illumina_read_2/NG-5257_test_read_2.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R1_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 0 is fetching file
/home/bastian/data/RAW/test1_GTCCGC_L008_R2_001_AC0RCJACXX.filt.fastq with lazy
loading (please wait...)
Rank 0 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with lazy
loading (please wait...)
Rank 0 is fetching file /home/bastian/data/RAW/PacBio/all_ccs.fastq with lazy
loading (please wait...)
*** stack smashing detected ***: Ray terminated
[ssb3:23288] *** Process received signal ***
[ssb3:23288] Signal: Segmentation fault (11)
[ssb3:23288] Signal code: (128)
[ssb3:23288] Failing at address: (nil)
I have no idea what's going on.
I doubt that I can run the assembly on my local machine, don't think I have
enough RAM here.
There shouldn't be any difference between the 2 machines, that's what puzzles
me.
Any ideas?
Bastian
________________________________________
From: Sébastien Boisvert [sebastien.boisver...@ulaval.ca]
Sent: Monday, August 26, 2013 3:12 PM
To: Hornung, Bastian
Cc: denovoassembler-users@lists.sourceforge.net
Subject: Re: [Denovoassembler-users] maximum read length for ray
On 26/08/13 04:56 AM, Hornung, Bastian wrote:
Hi @all,
I'd have a technical question about ray: What is the maximum read length, which
can be used?
I ask because I get a stack overflow (or rather a message that the process has
been aborted before it could happen) when I try to run ray with PacBio data (up
to 2kb in that set, IIRC), and wonder what the maximum is what ray can take.
It is 65536 nucleotides.
Best regards,
Bastian
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diff -bur stock/Ray-v2.2.0/code/SequencesLoader/SequencesLoader.cpp Ray-v2.2.0/code/SequencesLoader/SequencesLoader.cpp
--- stock/Ray-v2.2.0/code/SequencesLoader/SequencesLoader.cpp 2013-04-17 09:44:55.000000000 -0400
+++ Ray-v2.2.0/code/SequencesLoader/SequencesLoader.cpp 2013-08-27 10:29:30.830138632 -0400
@@ -201,6 +201,9 @@
m_loader.constructor(m_parameters->getMemoryPrefix().c_str(),m_parameters->showMemoryAllocations(),
m_rank);
+ char * seq = (char *) __Malloc(RAY_MAXIMUM_READ_LENGTH * sizeof(char), "CodePath/-amos", false);
+ char * qlt = (char *) __Malloc(RAY_MAXIMUM_READ_LENGTH * sizeof(char), "CodePath/-amos", false);
+
for(m_distribution_file_id=0;m_distribution_file_id<(int)allFiles.size();
m_distribution_file_id++){
@@ -212,11 +215,9 @@
// write Reads in AMOS format.
if(rank==MASTER_RANK&&m_parameters->useAmos()){
- char qlt[20000];
for(LargeIndex i=0;i<m_loader.size();i++){
ReadHandle iid=m_distribution_currentSequenceId;
m_distribution_currentSequenceId++;
- char seq[4000];
m_loader.at(i)->getSeq(seq,m_parameters->getColorSpaceMode(),true);
#ifdef ASSERT
assert(seq!=NULL);
@@ -237,6 +238,10 @@
}
m_loader.reset();
}
+
+ __Free(qlt, "/CodePath/-amos", false);
+ __Free(seq, "/CodePath/-amos", false);
+
m_loader.clear();
if(m_parameters->useAmos()){
fclose(fp);
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