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> 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://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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