Can you provide the last lines of the standard output ? On 06/12/13 10:15 PM, Sucheta Tripathy wrote: > Thanks Sebastian! I tried fixing that as well! Now both my libraries have > good quality equal number of sequences: Here is the content of > NumberOfSequences file: > > Files: 2 > > FileNumber: 0 > FilePath: /scratch/sucheta/out1.fastq > NumberOfSequences: 69393976 > FirstSequence: 0 > LastSequence: 69393975 > > FileNumber: 1 > FilePath: /scratch/sucheta/out2.fastq > NumberOfSequences: 69393976 > FirstSequence: 69393976 > LastSequence: 138787951 > > > Summary > NumberOfSequences: 138787952 > FirstSequence: 0 > LastSequence: 138787951 > ~ > > In the output directory, I see the following files: Where the > parallelPaths.txt file has 0 content. I am not sure what is making this crash. > > -rw-r--r-- 1 sucheta iicb 332 Dec 6 07:48 CoverageDistributionAnalysis.txt > -rw-r--r-- 1 sucheta iicb 259819 Dec 6 07:48 CoverageDistribution.txt > -rw-r--r-- 1 sucheta iicb 672 Dec 6 09:28 degreeDistribution.txt > -rw-r--r-- 1 sucheta iicb 1541 Dec 6 15:41 ElapsedTime.txt > -rw-r--r-- 1 sucheta iicb 164 Dec 6 06:23 FilePartition.txt > -rw-r--r-- 1 sucheta iicb 3545 Dec 6 09:27 GraphPartition.txt > -rw-r--r-- 1 sucheta iicb 6496 Dec 6 15:41 LibraryData.xml > -rw-r--r-- 1 sucheta iicb 389 Dec 6 15:41 LibraryStatistics.txt > -rw-r--r-- 1 sucheta iicb 2388 Dec 6 06:18 NetworkTest.txt > -rw-r--r-- 1 sucheta iicb 352 Dec 6 06:23 NumberOfSequences.txt > -rw-r--r-- 1 sucheta iicb 0 Dec 6 15:42 ParallelPaths.txt > drwxr-x--- 2 sucheta iicb 4096 Dec 6 16:20 Plugins > -rw-r--r-- 1 sucheta iicb 116 Dec 6 06:18 RayCommand.txt > -rw-r--r-- 1 sucheta iicb 18 Dec 6 06:18 RayPlatform_Version.txt > -rw-r--r-- 1 sucheta iicb 10 Dec 6 06:18 RayVersion.txt > drwxr-x--- 2 sucheta iicb 4096 Dec 6 06:18 Scheduling > -rw-r--r-- 1 sucheta iicb 25434 Dec 6 15:02 SeedLengthDistribution.txt > -rw-r--r-- 1 sucheta iicb 2859 Dec 6 06:23 SequencePartition.txt > > Here is my commandline: > mpiexec -n 96 Ray \ > -k \ > 21 \ > -p \ > /scratch/sucheta/out1.fastq \ > /scratch/sucheta/out2.fastq \ > -o \ > rayTest1 > ~ > > > > On Fri, Dec 6, 2013 at 9:10 PM, Sébastien Boisvert > <sebastien.boisver...@ulaval.ca <mailto:sebastien.boisver...@ulaval.ca>> > wrote: > > On 01/12/13 04:12 AM, Sucheta Tripathy wrote: > > > I am trying to run Ray for a while now on our Illumina data. It is > run in parallel mode and memory is not a constraint now because we have a > cluster with 16 X 16 GB memory in each node. > > > The problem is this: tmp1 and tmp2 don't contain the same number of > sequences. > > Using paired files with different number of sequences will cause crash in > Ray 2.2.0 and earlier versions. > If you use Ray 2.3.0, Ray will throw an error. > > > Also, lane1_1b and lane_1_2b are empty (0 sequences). You may want to > check that out too. > > > my Command: > mpiexec -n 64 Ray \ > -k \ > 31 \ > -disable-recycling \ > -p \ > /scratch/sucheta/tmp1.fastq \ > /scratch/sucheta/tmp2.fastq \ > -p \ > /scratch/sucheta/lane1_1b.fq \ > /scratch/sucheta/lane1_2b.fq \ > -o \ > rayTest > > Content of NumberOfSequences.txt > Files: 4 > > FileNumber: 0 > FilePath: /scratch/sucheta/tmp1.fastq > NumberOfSequences: 73013670 > FirstSequence: 0 > LastSequence: 73013669 > > FileNumber: 1 > FilePath: /scratch/sucheta/tmp2.fastq > NumberOfSequences: 72339350 > FirstSequence: 73013670 > LastSequence: 145353019 > > FileNumber: 2 > FilePath: /scratch/sucheta/lane1_1b.fq > NumberOfSequences: 0 > > FileNumber: 3 > FilePath: /scratch/sucheta/lane1_2b.fq > NumberOfSequences: 0 > > Summary > NumberOfSequences: 145353020 > FirstSequence: 0 > LastSequence: 145353019 > > > However, after running for a while Ray terminates: This is the last > few lines of STDOUT: > > --- > > Speed RAY_SLAVE_MODE_EXTENSION 1183 units/second > Rank 9: assembler memory usage: 850432 KiB > Rank 9 is changing direction. > Rank 12: assembler memory usage: 826944 KiB > Rank 12 starts on seed 1200, length is 477, flow 0 [1200/6451] > Rank 12 starts on seed 1201, length is 476, flow 0 [1201/6451] > Rank 10 traversed 1273646 nucleotide symbols > Rank 10: assembler memory usage: 869460 KiB > Rank 10 starts on seed 534, length is 906, flow 0 [534/6579] > Rank 31 reached 2270 vertices from seed 491, flow 1 > Speed RAY_SLAVE_MODE_EXTENSION 1174 units/second > Rank 31: assembler memory usage: 866768 KiB > Rank 31 is changing direction. > Rank 2 traversed 1910058 nucleotide symbols > Rank 2 reached 1269 vertices from seed 1007, flow 2 > Speed RAY_SLAVE_MODE_EXTENSION 1435 units/second > Rank 2: assembler memory usage: 843432 KiB > Rank 2 (extension done) NumberOfFlows: 2 > Rank 2 FlowedVertices: 0 576 1 1269 2 1269 > Rank 2: assembler memory usage: 839332 KiB > Rank 2 starts on seed 1008, length is 576, flow 0 [1008/6537] > Terminated > --- > > It creates the following output files before crashing: > > CoverageDistributionAnalysis.__txt NumberOfSequences.txt > CoverageDistribution.txt ParallelPaths.txt > degreeDistribution.txt Plugins > ElapsedTime.txt RayCommand.txt > FilePartition.txt RayPlatform_Version.txt > GraphPartition.txt RayVersion.txt > LibraryData.xml Scheduling > LibraryStatistics.txt SeedLengthDistribution.txt > NetworkTest.txt SequencePartition.txt > > > Any help in this regard will be much appreciated! > > > -- > Sucheta Tripathy, Ph.D > Scientist, Ramalingaswamy Fellow, > Indian Institute of Chemical Biology, > Kolkata, India. > https://sites.google.com/site/__suchetalab/ > <https://sites.google.com/site/suchetalab/> > https://twitter.com/tsucheta > > > > > > -- > Sucheta Tripathy, Ph.D > Scientist, Ramalingaswamy Fellow, > Indian Institute of Chemical Biology, > Kolkata, India. > https://sites.google.com/site/suchetalab/ > https://twitter.com/tsucheta
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