sebhtml/ray — Issue #44: Ray v1.7. Critial error found
Author: mscook
Created: 2012-02-07 02:04:09+00:00
State: open

Hi,

This may be a result of -
1) Poor cluster configuration
2) Stupidity on my part

BUT

Ray should halt immediately.

LOG:

Rank 6 is loading sequence reads
Rank 6 : partition is [8133607;9489207], 1355601 sequence reads
Rank 7 is loading sequence reads
Rank 7 : partition is [9489208;10844808], 1355601 sequence reads
Rank 1 is loading sequence reads
Rank 1 : partition is [1355602;2711202], 1355601 sequence reads
Rank 5 is loading sequence reads
Rank 5 : partition is [6778006;8133606], 1355601 sequence reads
Rank 3 is loading sequence reads
Rank 3 : partition is [4066804;5422404], 1355601 sequence reads
Rank 2 is loading sequence reads
Rank 2 : partition is [2711203;4066803], 1355601 sequence reads
Rank 4 is loading sequence reads
Rank 4 : partition is [5422405;6778005], 1355601 sequence reads
Rank 0 is loading sequence reads
Rank 0 : partition is [1;1355601], 1355601 sequence reads
Rank 9 is loading sequence reads
Rank 9 : partition is [12200410;13556010], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 9 has 0 sequence reads (completed)
Rank 13 is loading sequence reads
Rank 13 : partition is [17622814;18978414], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 13 has 0 sequence reads (completed)
Rank 10 is loading sequence reads
Rank 10 : partition is [13556011;14911611], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 10 has 0 sequence reads (completed)
Rank 11 is loading sequence reads
Rank 11 : partition is [14911612;16267212], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 11 has 0 sequence reads (completed)
Rank 12 is loading sequence reads
Rank 12 : partition is [16267213;17622813], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 12 has 0 sequence reads (completed)
Rank 15 is loading sequence reads
Rank 15 : partition is [20334016;21689626], 1355611 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 15 has 0 sequence reads (completed)
Rank 8 is loading sequence reads
Rank 8 : partition is [10844809;12200409], 1355601 sequence reads
Ray: cannot access 'XXXXX_proc.fastq': No such file or directory
Rank 8 has 0 sequence reads (completed)
Rank 14 is loading sequence reads
Rank 14 : partition is [18978415;20334015], 1355601 sequence reads

Running on 16 Processors across 2 nodes. The second node does not seem to have access to the input file.

Ray continues to run:

OutputNumbers.txt:
Contigs >= 100 nt
Number: 218
Total length: 5424549
Average: 24883
N50: 77874
Median: 4008
Largest: 203060
Contigs >= 500 nt
Number: 167
Total length: 5415213
Average: 32426
N50: 77874
Median: 11262
Largest: 203060
Scaffolds >= 100 nt
Number: 173
Total length: 5433800
Average: 31409
N50: 135589
Median: 3225
Largest: 376055
Scaffolds >= 500 nt
Number: 122
Total length: 5424464
Average: 44462
N50: 135589
Median: 8941
Largest: 376055

Results in discrepancy:

grep '>' Contigs.fasta | wc -l
107

"Contigs.fasta" 47454L, 2881955C
~2.9MB (5.4 reported)