HI Sebastian,
Thanks for developing this tool for users, I have heard many great things about
its potential
I am trying to assemble a Miseq paired end run with about 5 million reads of a
virus-enriched shotgun metagenome, and have used the following command to do
this (apologies for the long command details):
~/programs/Ray-2.3.0$ mpiexec -n 22 ray-build/Ray -o
~/projects/karen/analysis/raymeta_karen_4 -p
~/projects/karen/data/S86-B_S2_L001_R1_001.fastq
~/projects/karen/data/S86-B_S2_L001_R2_001.fastq -k 31 -search
~/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/NCBI-Finished-Bacterial-Genomes
-with-taxonomy
~/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/Genome-to-Taxon.tsv
~/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
~/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/Taxon-Names.tsv
-color-space
When I run this, things seem to process fine, but then I reach a point where
loading taxon begins, and I encounter a recurring error, which seems to stall
the analysis (over 48 hours) at a point where loadTree iteration printouts are
being made
The error that seems to be causing this is as follows
Error: parent and child are the same: 1 and 1
Im not sure what is causing this, and I have tried looking on the mailing list
archive to see if I could find whether anyone else has this problem, but no
luck so far. Any suggestions you could give me as to what I am doing wrong
would be greatly appreciated. I have pasted the last lines of the output below
Thanks patrick
Step: Loading taxons
Date: Fri Nov 22 17:23:18 2013
Elapsed time: 7 minutes, 56 seconds
Since beginning: 1 hours, 32 minutes, 27 seconds
***
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 13 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 16 loadTree iteration= 0 oldSize= 2643
newSize= 115644 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 8 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 4 loadTree iteration= 0 oldSize= 2643
newSize= 115644 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 7 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 14 loadTree iteration= 0 oldSize= 2643
newSize= 115644 Rank 11 loadTree iteration= 0 oldSize= 2643 newSize= 115644
Rank 19 loadTree iteration= 0 oldSize= 2643 newSize= 115644 Rank 3 loadTree
iteration= 0 oldSize= 2643 newSize= 115644 Rank 1 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 18 loadTree iteration= 0 oldSize= 2643
newSize= 115644 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 6 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 5 loadTree iteration= 0 oldSize= 2643
newSize= 115644 Rank 17 loadTree iteration= 0 oldSize= 2643 newSize= 115644
Rank 21 loadTree iteration= 0 oldSize= 2643 newSize= 115644 Rank 10 loadTree
iteration= 0 oldSize= 2643 newSize= 115644 Rank 20 loadTree iteration= 0
oldSize= 2643 newSize= 115644 Rank 15 loadTree iteration= 0 oldSize= 2643
newSize= 115644 Rank 2 loadTree iteration= 0 oldSize= 2643 newSize= 115644 Rank
9 loadTree iteration= 0 oldSize= 2643 newSize= 115644 Rank 12 loadTree
iteration= 0 oldSize= 2643 newSize= 115644 Rank 0 loadTree iteration= 0
oldSize= 2643 newSize= 115644 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 13 loadTree iteration= 1
oldSize= 115644 newSize= 115644 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 File
/home/plaffy/projects/karen/Paper-Replication-2012/Build-Input-Files-for-NCBI-Taxonomy/NCBI-taxonomy/TreeOfLife-Edges.tsv
has 1094669 entries
Error: parent and child are the same: 1 and 1 Rank 16 loadTree iteration= 1
oldSize= 115644 newSize= 115644 Rank 8 loadTree iteration= 1 oldSize= 115644
newSize= 115644 Rank 18 loadTree iteration= 1 oldSize= 115644 newSize= 115644
Rank 21 loadTree iteration= 1 oldSize= 115644 newSize= 115644 Rank 4 loadTree
iteration= 1 oldSize= 115644 newSize= 115644 Rank 14 loadTree iteration= 1
oldSize= 115644 newSize= 115644 Rank 3 loadTree iteration= 1 oldSize= 115644
newSize= 115644 Rank 6 loadTree iteration= 1 oldSize= 115644 newSize= 115644
Rank 17 loadTree iteration= 1 oldSize= 115644 newSize= 115644 Rank 11 loadTree
iteration= 1 oldSize= 115644 newSize= 115644 Rank 7 loadTree iteration= 1
oldSize= 115644 newSize= 115644 Rank 20 loadTree iteration= 1 oldSize= 115644
newSize= 115644 Rank 19 loadTree iteration= 1 oldSize= 115644 newSize= 115644
Rank 5 loadTree iteration= 1 oldSize= 115644 newSize= 115644 Rank 1 loadTree
iteration= 1 oldSize= 115644 newSize= 115644 Rank 10 loadTree iteration= 1
oldSize= 115644 newSize= 115644 Rank 15 loadTree iteration= 1 oldSize= 115644
newSize= 115644 Rank 2 loadTree iteration= 1 oldSize= 115644 newSize= 115644
Rank 9 loadTree iteration= 1 oldSize= 115644 newSize= 115644 Rank 12 loadTree
iteration= 1 oldSize= 115644 newSize= 115644 Rank 0 loadTree iteration= 1
oldSize= 115644 newSize= 115644
^Cmpiexec: killing job...
Dr Patrick Laffy
Postdoctoral Fellow: Genetic Bioinformaticist
Australian Institute of Marine Sciences
PMB No 3, Townsville MC, QLD 4810
ph: +61 7 4753 4365
web: www.aims.gov.au<https://webmail.aims.gov.au/owa/UrlBlockedError.aspx>
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