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abiswas-odu / Disco

Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler
GNU General Public License v3.0
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runDisco-MPI.sh cat error #1

Closed plpla closed 7 years ago

plpla commented 7 years ago

Error at the end of the assembly with runDisco-MPI.sh

cat: Sample_D1024-Disco/assembly/Sample_D1024-DiscocontigsFinal.fasta: No such file or directory cat: Sample_D1024-Disco/assembly/Sample_D1024-DiscoscaffoldsFinal.fasta: No such file or directory

The files are: Sample_D1024-Disco/assembly/Sample_D1024-Disco_contigsFinalCombined.fasta and Sample_D1024-Disco/assembly/ Sample_D1024-Disco_scaffoldsFinalCombined.fasta

plpla commented 7 years ago

The issue seems to start way before the cat command. From the log file:

Function start: OverlapGraph()
Load edge file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt

Exit from File: ../src/OverlapGraphSimple.cpp Line: 534 Function: loadParEdgesFromEdgeFile()
Message: Unable to open file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt
abiswas-odu commented 7 years ago

Will it be possible to post the complete log file? It will help me to find where the error occurred.

plpla commented 7 years ago

Here it is:

--------------------------------------------------------------------------
WARNING: a request was made to bind a process. While the system
supports binding the process itself, at least one node does NOT
support binding memory to the process location.

  Node:  r107-n89

This is a warning only; your job will continue, though performance may
be degraded.
--------------------------------------------------------------------------
Software: Disco Assembler (Distributed Computation) [November 2016]
Version : 1.0
Developed by: Biswas, Abhishek; Pan, Chongle et.al.
Affiliation: Oak Ridge National Lab / University of Tennessee
Rank 0 running on r107-n89 with 8 threads.
Max available memory: 23 GB
PRINTING ARGUMENTS
/rap/SOME_PATH/software2/Disco/buildG-MPI -pe Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz,Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz -f Sample_D1024-Disco/graph/Sample_D1024-Disco -s Sample_D1024-Disco/assembly/Sample_D1024-Disco -simPth /rap/SOME_PATH/software2/Disco -p /rap/SOME_PATH/software2/Disco/disco.cfg -t 8 -m 23 
Max usable memory: 23 GB
Currently in file: ../src/Dataset.cpp Function: readDataset()
Reading dataset: 0 from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz

Dataset:  0
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
     32902 good reads in current dataset.
        26 bad reads in current dataset.
     32928 total reads in current dataset.
     32902 good reads in all datasets.

Function readDataset() finished in 1.40615 Seconds.
Memory used: 26 - 22 = 4 MB.

Currently in file: ../src/Dataset.cpp Function: readDataset()
Reading dataset: 1 from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz

Dataset:  1
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
     32861 good reads in current dataset.
        67 bad reads in current dataset.
     32928 total reads in current dataset.
     65763 good reads in all datasets.

Function readDataset() finished in 1.3876 Seconds.
Memory used: 31 - 26 = 5 MB.

Shortest read length in all datasets:   250
 Longest read length in all datasets:   250
Currently in file: ../src/HashTable.cpp Function: insertDataset()
Hash Table size set to: 1114523
Currently in file: ../src/HashTable.cpp Function: populateReadLengths()
Currently in file: ../src/HashTable.cpp Function: readReadLengthsFromFile()
Reading read lengths from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
     32902 good reads in current file.
        26 bad reads in current file.
     32928 total reads in current file.
Function readReadLengthsFromFile() finished in 0.337105 Seconds.
Memory used: 48 - 48 = 0 MB.

Currently in file: ../src/HashTable.cpp Function: readReadLengthsFromFile()
Reading read lengths from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
     32861 good reads in current file.
        67 bad reads in current file.
     32928 total reads in current file.
Function readReadLengthsFromFile() finished in 0.33465 Seconds.
Memory used: 48 - 48 = 0 MB.

Function populateReadLengths() finished in 0.671959 Seconds.
Memory used: 48 - 48 = 0 MB.

Hash Data size set to: 1183734
Currently in file: ../src/HashTable.cpp Function: populateReadData()
Currently in file: ../src/HashTable.cpp Function: readReadSequenceFromFile()
Reading read data from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
     32902 good reads in current file.
        26 bad reads in current file.
     32928 total reads in current file.
Function readReadSequenceFromFile() finished in 0.513898 Seconds.
Memory used: 65 - 65 = 0 MB.

Currently in file: ../src/HashTable.cpp Function: readReadSequenceFromFile()
Reading read data from file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
File name: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
     32861 good reads in current file.
        67 bad reads in current file.
     32928 total reads in current file.
Function readReadSequenceFromFile() finished in 0.513951 Seconds.
Memory used: 65 - 65 = 0 MB.

Function populateReadData() finished in 1.03094 Seconds.
Memory used: 57 - 57 = 0 MB.

Function insertDataset() finished in 1.71086 Seconds.
Memory used: 57 - 39 = 18 MB.

Currently in file: ../src/OverlapGraph.cpp Function: buildOverlapGraphFromHashTable()
Currently in file: ../src/OverlapGraph.cpp Function: markContainedReads()
Proc:0 Searching contained reads for range: (1,65763)
[r107-n89:27699] *** Process received signal ***
[r107-n89:27699] Signal: Segmentation fault (11)
[r107-n89:27699] Signal code:  (128)
[r107-n89:27699] Failing at address: (nil)
[r107-n89:27699] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x2b9e8d9997e0]
[r107-n89:27699] [ 1] /software6/mpi/openmpi/1.8.1_intel/lib/libopen-pal.so.6(opal_memory_ptmalloc2_int_free+0x74)[0x2b9e8fbb9eb4]
[r107-n89:27699] [ 2] /software6/mpi/openmpi/1.8.1_intel/lib/libopen-pal.so.6(opal_memory_ptmalloc2_free+0xb0)[0x2b9e8fbbbbc0]
[r107-n89:27699] [ 3] /rap/SOME_PATH/software2/Disco/buildG-MPI[0x422597]
[r107-n89:27699] [ 4] /rap/SOME_PATH/software2/Disco/buildG-MPI[0x414d50]
[r107-n89:27699] [ 5] /rap/SOME_PATH/software2/Disco/buildG-MPI[0x41482f]
[r107-n89:27699] [ 6] /rap/SOME_PATH/software2/Disco/buildG-MPI[0x42843a]
[r107-n89:27699] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd)[0x2b9e8dbc5d1d]
[r107-n89:27699] [ 8] /rap/SOME_PATH/software2/Disco/buildG-MPI[0x405789]
[r107-n89:27699] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 27699 on node r107-n89 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
PRINTING ARGUMENTS
/rap/SOME_PATH/software2/Disco/fullsimplify -fp Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz,Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz -e Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_3_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_4_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_5_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_6_parGraph.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_7_parGraph.txt -crd Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_3_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_4_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_5_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_6_containedReads.txt,Sample_D1024-Disco/graph/Sample_D1024-Disco_0_7_containedReads.txt -simPth /rap/SOME_PATH/software2/Disco -p /rap/SOME_PATH/software2/Disco/disco.cfg -p2 /rap/SOME_PATH/software2/Disco/disco_2.cfg -p3 /rap/SOME_PATH/software2/Disco/disco_3.cfg -o Sample_D1024-Disco/assembly/Sample_D1024-Disco -t 8 -log DEBUG4 
File(s) including reads: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz      Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz       
File(s) including edges: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt   Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_parGraph.txt    Sample_D1024-Disco/graph/Sample_D1024-Disco_0_3_parGraph.txt    Sample_D1024-Disco/graph/Sample_D1024-Disco_0_4_parGraph.txt    Sample_D1024-Disco/graph/Sample_D1024-Disco_0_5_parGraph.txt    Sample_D1024-Disco/graph/Sample_D1024-Disco_0_6_parGraph.txt    Sample_D1024-Disco/graph/Sample_D1024-Disco_0_7_parGraph.txt    
Output file names' prefix is: Sample_D1024-Disco/assembly/Sample_D1024-Disco

>>> Function start: main()

>>> Function start: DataSet()

>>> Function start: loadReadLenghtsFromReadFile()
load reads from read file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R1_001.fastq.gz
     32928 read lengths loaded from this read file
<<< Function stop: loadReadLenghtsFromReadFile(), Elapsed time: 0.234763 seconds, Memory usage: 6 - 4 = 2 MB.
----

>>> Function start: loadReadLenghtsFromReadFile()
load reads from read file: Sample_D1024/D1024_TAAGGCGA-TAGATCGC_L001_R2_001.fastq.gz
     32928 read lengths loaded from this read file
<<< Function stop: loadReadLenghtsFromReadFile(), Elapsed time: 0.231924 seconds, Memory usage: 9 - 6 = 3 MB.
----
<<< Function stop: DataSet(), Elapsed time: 0.467332 seconds, Memory usage: 8 - 4 = 4 MB.
----

>>> Function start: storeContainedReadInformation()
Store contained read information...
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_3_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_4_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_5_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_6_containedReads.txt
Processing:Sample_D1024-Disco/graph/Sample_D1024-Disco_0_7_containedReads.txt
Total number of contained reads loaded from read file(s): 9289
<<< Function stop: storeContainedReadInformation(), Elapsed time: 0.0468504 seconds, Memory usage: 8 - 8 = 0 MB.
----
Total number of unique reads loaded from read file(s): 65856
Log level is 7: DEBUG4
Minimum overlap length is: 30
Maximum read count in dead-end edge is: 2
Maximum edge length in dead-end edge is: 200
Minimum read count in edges with flow is: 5
Minimum edge length of edges with flow is: 500
Minimum edge length for edges to be reported is: 500
Minimum overlap length difference for branches to clip: 10
Minimum fold difference to consider branches to be short: 2

>>> Function start: SimplifyGraph()
Graph Simplification Iteration: 1

>>> Function start: OverlapGraph()
Load edge file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt

Exit from File: ../src/OverlapGraphSimple.cpp Line: 534 Function: loadParEdgesFromEdgeFile()
Message: Unable to open file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_1_parGraph.txt

>>> Function start: readParEdges()

Exit from File: ../src/OverlapGraph.cpp Line: 1968 Function: readParEdges()
Message: Unable to open file: Sample_D1024-Disco/assembly/Sample_D1024-Disco_0_ParSimpleEdges.txt
Load edge file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_parGraph.txt

Exit from File: ../src/OverlapGraphSimple.cpp Line: 534 Function: loadParEdgesFromEdgeFile()
Message: Unable to open file: Sample_D1024-Disco/graph/Sample_D1024-Disco_0_2_parGraph.txt
abiswas-odu commented 7 years ago

Fixed segmentation bug when running MPI version with single node. Master branch updated. Fix will be included in full release.