On 25/11/13 06:36 PM, Patrick Laffy wrote: > HI Sebastian, Hi Patrick,
I patched the code so that the message "Error: parent and child are the same: x and x" is instead reported as a warning (and also only once for any invalid edge). https://github.com/sebhtml/ray/commit/2e79260e29e04fc84c12767ea2acb1723eae8a27 > > 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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