Step 1 error

[GideonPisanty]

I am trying to run the first step, but the program always exits with the same error.

This is the command I am running:

#!/bin/sh
#$ -S /bin/bash
BINNING_HOME=/isilon/ottawa-rdc/users/pisantyg/binning-master/
source ~/miniconda3/bin/activate
$BINNING_HOME/makecommands.compatibility.sh /isilon/ottawa-rdc/users/pisantyg/data/8_binning/genes_dir/ 50 /isilon/ottawa-rdc/users/pisantyg/data/8_binning/pairwise_output/ RAxML_bootstrap.final

And this is the error I get:

/isilon/ottawa-rdc/users/pisantyg/binning-master//makecommands.compatibility.sh: line 20: 20950 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both

Thank you for your help.

[smirarab]

Gideon, there should be more in the standard error. Would you be able to capture the rest of your standard error and provide? Use:

$BINNING_HOME/makecommands.compatibility.sh /isilon/ottawa-rdc/users/pisantyg/data/8_binning/genes_dir/ 50 /isilon/ottawa-rdc/users/pisantyg/data/8_binning/pairwise_output/ RAxML_bootstrap.final 2>sometempfile.log

and provide sometempfile.log.

Thanks

[GideonPisanty]

Thank you for the reply. I ran the new command and here is the output:

Traceback (most recent call last):
File "/isilon/ottawa-rdc/users/pisantyg/binning-master//remove_edges_from_tree.py", line 38, in
edges = tree.get_edge_set(filt)
AttributeError: 'Tree' object has no attribute 'get_edge_set'

[GideonPisanty]

I see there is a previous issue with this output - so I should use an earlier version of dendropy?

[smirarab]

Yes, please note the requirements:

https://github.com/smirarab/binning#requirements

[GideonPisanty]

Thank you

[GideonPisanty]

I downgraded dendropy and it still doesn't work. The error message has changed back to the first one:

/isilon/ottawa-rdc/users/pisantyg/binning-master//makecommands.compatibility.sh: line 20: 31861 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both

I am grateful for your help!

[smirarab]

Can you again do it with standard error captured and send me the standard error? See my previous post on how to capture standard error.

[GideonPisanty]

I did it with the error capture and got this output in the error file:

/isilon/ottawa-rdc/users/pisantyg/binning-master//makecommands.compatibility.sh: line 20: 31861 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both

Thank you.

[GideonPisanty]

I thought maybe I am not defining the BINNINGHOME environmental variable correctly? I just defined it in the SH execution file, like this:

#!/bin/sh
#$ -S /bin/bash
BINNING_HOME=/isilon/ottawa-rdc/users/pisantyg/binning-master/
source ~/miniconda3/bin/activate
$BINNING_HOME/makecommands.compatibility.sh /isilon/ottawa-rdc/users/pisantyg/data/8_binning/genes_dir/ 50 /isilon/ottawa-rdc/users/pisantyg/data/8_binning/pairwise_output/ RAxML_bootstrap.final

Do I also need to define it via PATH?

[smirarab]

Try:

export BINNING_HOME=/isilon/ottawa-rdc/users/pisantyg/binning-master/

[GideonPisanty]

Thanks. I tried it now, but nothing has changed.

[GideonPisanty]

Dear Prof. Mirarab

Do you have any further suggestions how to solve this issue? I tried to run the program from a cluster and from a VBox and got exactly the same error either way. I would really like to conduct this analysis. Thank you so much.

[GideonPisanty]

In case it wasn't clear, this is the output of sometempfile:

/isilon/ottawa-rdc/users/pisantyg/binning-master//makecommands.compatibility.sh: line 20: 31861 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both

Thank you

[smirarab]

Gideon, There is no information in what you have pasted that can help me debug. Can you just send me (through my personal email; not here) your input files? I can try to run and see what I get. Thanks Siavash

…

On Fri, Feb 8, 2019 at 1:11 PM Gideon Pisanty ***@***.***> wrote: In case it wasn't clear, this is the output of sometempfile: /isilon/ottawa-rdc/users/pisantyg/binning-master// makecommands.compatibility.sh: line 20: 31861 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both Thank you — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAybuB1VAAFfRKqpn1_vlw3zeOXljWVsks5vLb3lgaJpZM4ZBXvz> .

-- Siavash Mirarab

[GideonPisanty]

Dear Siavash I greatly appreciate your help! I am out of the office until the beginning of March and I don't have access to the data. As soon as I am back I will send you the files. Thank you so much. Gideon  Gideon Pisanty Post-doctoral fellowCanadian National Collection of Insects (CNC)/Collection nationale canadienne d'insects (CNC)Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada960 Carling Avenue, Ottawa, Ontario, CANADA K1A 0C6Telephone/Téléphone: 613-759-6369Facsimile/Télécopieur: 613-759-1701gidpisa79@yahoo.comgideon.pisanty@canada.ca     From: Siavash Mirarab <notifications@github.com> To: smirarab/binning <binning@noreply.github.com> Cc: Gideon Pisanty <gidpisa79@yahoo.com>; Author <author@noreply.github.com> Sent: Wednesday, February 13, 2019 6:10 PM Subject: Re: [smirarab/binning] Step 1 error (#5) Gideon, There is no information in what you have pasted that can help me debug. Can you just send me (through my personal email; not here) your input files? I can try to run and see what I get. Thanks Siavash

…

On Fri, Feb 8, 2019 at 1:11 PM Gideon Pisanty ***@***.***> wrote: In case it wasn't clear, this is the output of sometempfile: /isilon/ottawa-rdc/users/pisantyg/binning-master// makecommands.compatibility.sh: line 20: 31861 Killed python $BINNING_HOME/remove_edges_from_tree.py $all.full $support $all -strip-both Thank you — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#5 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAybuB1VAAFfRKqpn1_vlw3zeOXljWVsks5vLb3lgaJpZM4ZBXvz> .

-- Siavash Mirarab — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.