On 02/12/13 07:37 PM, Patrick Laffy wrote: > Hi again, > > Thanks Pier-Luc for your responses to my queries, but so far I still keep > encountering the same issue. I have tried twice now to redownload the files. > Im reticent to delete the lines without knowing what the flow-on consequences > for doing this, I guess I will have to wait and see what Sebastien says when > he responds to this email
Hi, As Pier-Luc highlighted, it is because there is a line with a parent being its own child. However, I checked the code and this is mostly just a notice -- the run will continue; it won't stop because of this. Such entries are just skipped. > > Thanks, > > Patrick > > *From:*Pier-Luc Plante [mailto:[email protected]] > *Sent:* Friday, 29 November 2013 2:36 AM > *To:* [email protected]; Patrick Laffy > *Subject:* Re: [Denovoassembler-users] FW: error issues: Parent and child are > the same: 1 and 1 > > Hi, > I suggest you regenerate the treeoflife-edges.tsv file from beginning > (re-download the files). You could also try to download an older version if > it is available. > If that doesn't solve the issue, you could consider deleting the lines where > the left and the right values are the same but I am not sure this is the best > way to solve the issue. > This files is used to generate the Tree of Life. Unfortunately, I don't know > if these lines are error that can be deleted or error that need to be > corrected to construct the tree. > The other solution is to wait for Sebastien to come back and answer you. > > Pier-Luc > > Le 2013-11-27 18:45, Patrick Laffy a écrit : > > Thanks Pier-luc > > There are several, which I guess would explain this issue, however, im > not really sure how to deal with this data. I know the treeoflife-edges.tsv > file is generated from the nodes.dmp file that is in the uncompressed taxdump > nodes folder, but I suspect its not appropriate to go fiddling around with > the values in this file. Im not really sure what the context of this > information is, so its hard to say what changing things in this file will > achieve. > > Do you have any suggestion as to how I can deal with this issue. > > Thanks > > Patrick > > *From:*Pier-Luc Plante [mailto:[email protected]] > *Sent:* Wednesday, 27 November 2013 12:48 AM > *To:* [email protected] > <mailto:[email protected]> > *Subject:* Re: [Denovoassembler-users] FW: error issues: Parent and child > are the same: 1 and 1 > > 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 : > > -- > > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > 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. 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