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smirarab / binning

Code for statistical binning and related scripts
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Step 1 error #5

Open GideonPisanty opened 5 years ago

GideonPisanty commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

smirarab commented 5 years ago

Yes, please note the requirements:

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

GideonPisanty commented 5 years ago

Thank you

GideonPisanty commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

Try:

export BINNING_HOME=/isilon/ottawa-rdc/users/pisantyg/binning-master/
GideonPisanty commented 5 years ago

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

GideonPisanty commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 notifications@github.com 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 https://github.com/smirarab/binning/issues/5#issuecomment-461894370, or mute the thread https://github.com/notifications/unsubscribe-auth/AAybuB1VAAFfRKqpn1_vlw3zeOXljWVsks5vLb3lgaJpZM4ZBXvz .

-- Siavash Mirarab

GideonPisanty commented 5 years ago

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 notifications@github.com 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 https://github.com/smirarab/binning/issues/5#issuecomment-461894370, 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.

sugarcane1989 commented 5 years ago

Dear Dr Siavash, I am Bai Lin and I work in Kunming Institute of Botany, Chinese Academy of Sciences. I have also received the same error report like Dr GideonPisanty.

**" File "/ds3200_1/users_root/lidezhu/bailin/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'".**

As you said up there, this problem might relate to my Dendropy version. I have installered Dendropy 3.12.1; however our lab has Dendropy 4.4.0 and it is added in the environmental variable. Can you please teach me how to make sure when I use your scripts, they use Dendropy 3.12.1. Thank you very much! Best wishes, Bai Lin

smirarab commented 5 years ago

You need the version 3.12.1 to have higher precedence. It really depends on your setting. Does this help?

https://medium.com/@trstringer/module-import-precedence-in-python-acad7e0bd57

On Mon, Aug 12, 2019 at 12:14 AM sugarcane1989 notifications@github.com wrote:

Dear Dr Siavash, I am Bai Lin and I work in Kunming Institute of Botany, Chinese Academy of Sciences. I have also received the same error report like Dr GideonPisanty.

***" File "/ds3200_1/users_root/lidezhu/bailin/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'".*

As you said up there, this problem might relate to my Dendropy version. I have installered Dendropy 3.12.1; however our lab has Dendropy 4.4.0 and it is added in the environmental variable. Can you please teach me how to make sure when I use your scripts, they use Dendropy 3.12.1. Thank you very much! Best wishes, Bai Lin

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/smirarab/binning/issues/5?email_source=notifications&email_token=AAGJXOGRSTQRJ4IKAYDW4P3QEEEUJA5CNFSM4GIFPPZ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4BXETA#issuecomment-520319564, or mute the thread https://github.com/notifications/unsubscribe-auth/AAGJXOACXQF5UB6H2VQGD3LQEEEUJANCNFSM4GIFPPZQ .

-- Siavash Mirarab

sugarcane1989 commented 5 years ago

Dear Dr Siavash, Thank you very much for your explaination. I will try the method you mentioned. Best wishes, Bai Lin