Re: [Denovoassembler-users] FW: error issues: Parent and child are the same: 1 and 1

[Pier-Luc Plante]

Hi, I am not Sebastian, but i can try to help you! The error i related to the TreeOfLife-Edges.tsv file. This file contains 2 columns. ex: 1       131567 131567  2 2       201174 201174  1760 1760    84992 84992   84993 84993   255726 Can you check if there is a line in the file where the value in the left column is the same as the one in the right column? Pier-Luc Le 2013-11-25 18:36, Patrick Laffy a écrit :   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   --  The information contained within this transmission is for the use of the intended recipient only and may contain confidential and/or legally privileged material and/or material the subject of copyright and/or personal information and/or sensitive information that is subject to the Privacy Act 1988. Any review, re-transmission, disclosure, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipient is prohibited. If you have received this email in error please notify the AIMS Privacy Officer on (07) 4753 4444 and delete all copies of this transmission together with any attachments.

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