Illegal division by zero at parse-table line 664

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Rob

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Apr 17, 2020, 4:20:47 PM4/17/20
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I am trying to generate a circos image from tabular data through a conda install of circos-tools with the following code:

cat data/antismash_summary.txt | parse-table > output/tmp.txt

but I am getting the following error:

Illegal division by zero at /home/lamma/miniconda3/envs/ciros/bin/parse-table line 664, <STDIN> line 1

I also tried without the cat but get the same error:

parse-table antismash_summary.txt > output/tmp.txt

Any help would be apriciated :)

\"\Undefine\"

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Apr 17, 2020, 5:05:46 PM4/17/20
to circos-data-visualization
parse-table -file yourfile-name

---Original---
From: "Rob"<Rmm...@outlook.com>
Date: 2020/4/18 04:20:51
Subject: [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 17, 2020, 7:38:14 PM4/17/20
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I get the same error when using this


On Friday, April 17, 2020 at 11:05:46 PM UTC+2, \"\Undefine\" wrote:
parse-table -file yourfile-name

---Original---
From: "Rob"<Rmm...@outlook.com>
Date: 2020/4/18 04:20:51
Subject: [circos] Illegal division by zero at parse-table line 664

I am trying to generate a circos image from tabular data through a conda install of circos-tools with the following code:

cat data/antismash_summary.txt | parse-table > output/tmp.txt

but I am getting the following error:

Illegal division by zero at /home/lamma/miniconda3/envs/ciros/bin/parse-table line 664, <STDIN> line 1

I also tried without the cat but get the same error:

parse-table antismash_summary.txt > output/tmp.txt

Any help would be apriciated :)

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\"\Undefine\"

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Apr 19, 2020, 12:10:26 AM4/19/20
to circos-data-visualization

Maybe you should check the separator character in your file,
Use parse-table to read file, you must ensure that the file can be accepted.
for example:
A B C D
a b c d
1 2 3 4
There is a separator between data columns
You can try to replace all the separators in your file with tabs(Tab key)

Hope useful

------------------ 原始邮件 ------------------
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发送时间: 2020年4月18日(星期六) 凌晨5:15
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主题: Re: [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 21, 2020, 8:51:45 AM4/21/20
to Circos
The table I am using has worked on the webserveversion, any reason why it would not work on the local version?


On Sunday, 19 April 2020 06:10:26 UTC+2, \"\Undefine\" wrote:
Maybe you should check the separator character in your file,
Use parse-table to read file, you must ensure that the file can be accepted.
for example:
A B C D
a b c d
1 2 3 4
There is a separator between data columns
You can try to replace all the separators in your file with tabs(Tab key)

Hope useful

------------------ 原始邮件 ------------------
发件人: "Rob"<rob.m...@gmail.com>;
发送时间: 2020年4月18日(星期六) 凌晨5:15
主题: Re: [circos] Illegal division by zero at parse-table line 664

I get the same error when using this

On Friday, April 17, 2020 at 11:05:46 PM UTC+2, \"\Undefine\" wrote:
parse-table -file yourfile-name

---Original---
From: "Rob"<Rmm...@outlook.com>
Date: 2020/4/18 04:20:51
Subject: [circos] Illegal division by zero at parse-table line 664

I am trying to generate a circos image from tabular data through a conda install of circos-tools with the following code:

cat data/antismash_summary.txt | parse-table > output/tmp.txt

but I am getting the following error:

Illegal division by zero at /home/lamma/miniconda3/envs/ciros/bin/parse-table line 664, <STDIN> line 1

I also tried without the cat but get the same error:

parse-table antismash_summary.txt > output/tmp.txt

Any help would be apriciated :)

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\"\Undefine\"

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Apr 21, 2020, 10:24:34 AM4/21/20
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can you send me a copy of your file?


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月21日(星期二) 晚上8:51
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主题: Re: 回复： [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 21, 2020, 10:41:42 AM4/21/20
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Here is a copy of the table :)


On Tuesday, 21 April 2020 16:24:34 UTC+2, \"\Undefine\" wrote:
can you send me a copy of your file?


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月21日(星期二) 晚上8:51
antismash_summary.txt

\"\Undefine\"

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Apr 21, 2020, 10:58:43 AM4/21/20
to circos-data-visualization
I read the document on the official website and found relevant contents
first, we use the `make-table` to get random data
make-table -rows 4 -col 3 -brief > table.txt
The data are as follows：
then, let's see
so，You have to make sure your data is all numbers！！！

Hope useful

good luck to you.

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月21日(星期二) 晚上10:41
收件人: "Circos"<circos-data-...@googlegroups.com>;
主题: Re: 回复： 回复： [circos] Illegal division by zero at parse-table line 664
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59C32423@C241B64C.190A9F5E.jpg
3001E70D@C7452439.190A9F5E.jpg
2D01E706@C0BAB737.190A9F5E.jpg

Rob

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Apr 21, 2020, 11:14:15 AM4/21/20
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I will try this thank you. The webserver states to use - for NULL values so that is why they are there. This is an odd inconsistency if it is the case!


On Tuesday, April 21, 2020 at 4:58:43 PM UTC+2, \"\Undefine\" wrote:
I read the document on the official website and found relevant contents
first, we use the `make-table` to get random data
make-table -rows 4 -col 3 -brief > table.txt
The data are as follows：
then, let's see
so，You have to make sure your data is all numbers！！！

Hope useful

good luck to you.

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月21日(星期二) 晚上10:41

Rob

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Apr 22, 2020, 3:48:29 AM4/22/20
to Circos
Now the tool has suddenly stopped working and is pushing this error out:
Can't locate Config/General.pm in @INC (you may need to install the Config::General module)



On Tuesday, 21 April 2020 16:58:43 UTC+2, \"\Undefine\" wrote:
I read the document on the official website and found relevant contents
first, we use the `make-table` to get random data
make-table -rows 4 -col 3 -brief > table.txt
The data are as follows：
then, let's see
so，You have to make sure your data is all numbers！！！

Hope useful

good luck to you.

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月21日(星期二) 晚上10:41

\"\Undefine\"

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Apr 22, 2020, 4:15:04 AM4/22/20
to circos-data-visualization
This means that the General module is miss on your marchine, I'm sorry I don't know much about this.
Maybe you can try using the following command:
cpanm Config::General
or
perl -MCPAN -e shell
install Config::General
It is worth mentioning that I do not recommend using the commands I provided directly. I suggest you go to the official website to see the details and try


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午3:48
收件人: "Circos"<circos-data-...@googlegroups.com>;
主题: Re: 回复： 回复： 回复： [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 22, 2020, 4:42:10 AM4/22/20
to Circos
It is weird it was workin gyesterday though and now suddenly it is not. I have tried to install all th emissing packages, but Circos is not recognising all of them as being installed.

circos -modules
missing            GD
missing            GD::Polyline

Yet trying to install these modules yeilds:
cpanm GD
GD is up to date. (2.71)
 cpanm GD::Polyline
GD::Polyline is up to date. (0.2)

So I am not really sure what to do.

On Wednesday, 22 April 2020 10:15:04 UTC+2, \"\Undefine\" wrote:
This means that the General module is miss on your marchine, I'm sorry I don't know much about this.
Maybe you can try using the following command:
cpanm Config::General
or
perl -MCPAN -e shell
install Config::General
It is worth mentioning that I do not recommend using the commands I provided directly. I suggest you go to the official website to see the details and try


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午3:48

\"\Undefine\"

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Apr 22, 2020, 4:54:24 AM4/22/20
to circos-data-visualization
I think there are several possibilities:
1. Environment
2. Path
3. Permission
Maybe you can check the running environment and permission.

There is also a worst case scenario, uninstall and then reinstall.

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午4:42
收件人: "Circos"<circos-data-...@googlegroups.com>;
主题: Re: 回复： 回复： 回复： 回复： [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 22, 2020, 5:59:04 AM4/22/20
to Circos
Do you mean conda environment or when my env dircrectory is located and I what permissions?


On Wednesday, 22 April 2020 10:54:24 UTC+2, \"\Undefine\" wrote:
I think there are several possibilities:
1. Environment
2. Path
3. Permission
Maybe you can check the running environment and permission.

There is also a worst case scenario, uninstall and then reinstall.

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午4:42

\"\Undefine\"

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Apr 22, 2020, 6:12:04 AM4/22/20
to circos-data-visualization
yes, 
If you use conda to install circos, before the installation, need create a new environment to keep it independent, prevent damage to the local environment.
then when using circos, you need to activate the circos environment frist. 
you can using the following command:
`conda env list`
to view the environment
`source activate env_name`
to activate env

if it is insufficient permission, you can try the administrator account.


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午5:59
收件人: "Circos"<circos-data-...@googlegroups.com>;
主题: Re: 回复： 回复： 回复： 回复： 回复： [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 22, 2020, 6:14:17 AM4/22/20
to Circos
There would be no reason the conda environment has any differing permission to my many other ones so I don't see that being an issue. The problem seems to be the detection of Perl modules which I have tried to install both through perl and conda.


On Wednesday, 22 April 2020 12:12:04 UTC+2, \"\Undefine\" wrote:
yes, 
If you use conda to install circos, before the installation, need create a new environment to keep it independent, prevent damage to the local environment.
then when using circos, you need to activate the circos environment frist. 
you can using the following command:
`conda env list`
to view the environment
`source activate env_name`
to activate env

if it is insufficient permission, you can try the administrator account.


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 下午5:59

\"\Undefine\"

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Apr 22, 2020, 6:33:28 AM4/22/20
to circos-data-visualization
At present, this is the last and most effective way。

------------------ 原始邮件 ------------------
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发送时间: 2020年4月22日(星期三) 晚上6:14
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Rob

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Apr 22, 2020, 6:41:27 AM4/22/20
to Circos
That being a fresh install? I will try :)


On Wednesday, 22 April 2020 12:33:28 UTC+2, \"\Undefine\" wrote:
At present, this is the last and most effective way。

------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 晚上6:14

\"\Undefine\"

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Apr 22, 2020, 6:47:56 AM4/22/20
to circos-data-visualization
I'm sorry I didn't help you -.-

good luck


------------------ 原始邮件 ------------------
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发送时间: 2020年4月22日(星期三) 晚上6:41
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Rob

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Apr 22, 2020, 10:04:38 AM4/22/20
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Okay so Circos is abck and working yay :) Now having changed all values in the table to be numbers I still get the same error message.


On Wednesday, 22 April 2020 12:47:56 UTC+2, \"\Undefine\" wrote:
I'm sorry I didn't help you -.-

good luck


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 晚上6:41

\"\Undefine\"

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Apr 22, 2020, 8:23:12 PM4/22/20
to circos-data-visualization
You try this test data:
data E F G
A 141 169 236
B 19 80 88
C 61 124 74
D 79 191 16
I suspect it's because the data is to be calculated, such as division.
so make surethat there is no 0 in the data（numerator、denominator）.
If the test data works, that's right...


------------------ 原始邮件 ------------------
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发送时间: 2020年4月22日(星期三) 晚上10:04
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主题: Re: 回复： 回复： 回复： 回复： 回复： 回复： 回复： 回复： [circos] Illegal division by zero at parse-table line 664
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Rob

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Apr 23, 2020, 2:37:50 AM4/23/20
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Then how is one meant to represent NA in the data, the website says use '-' but you previously said all data much be numberic?


On Thursday, 23 April 2020 02:23:12 UTC+2, \"\Undefine\" wrote:
You try this test data:
data E F G
A 141 169 236
B 19 80 88
C 61 124 74
D 79 191 16
I suspect it's because the data is to be calculated, such as division.
so make surethat there is no 0 in the data（numerator、denominator）.
If the test data works, that's right...


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 晚上10:04

Rob

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Apr 23, 2020, 3:34:26 AM4/23/20
to Circos
So it seems that parse-table is not actually parsing the table. I tried to generate some example data with make-table but is give no output. Any idea why the tools are just not working?


On Thursday, 23 April 2020 02:23:12 UTC+2, \"\Undefine\" wrote:
You try this test data:
data E F G
A 141 169 236
B 19 80 88
C 61 124 74
D 79 191 16
I suspect it's because the data is to be calculated, such as division.
so make surethat there is no 0 in the data（numerator、denominator）.
If the test data works, that's right...


------------------ 原始邮件 ------------------
发件人: "Rob"<Rmm...@outlook.com>;
发送时间: 2020年4月22日(星期三) 晚上10:04

Shree

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Mar 23, 2023, 4:53:42 PM3/23/23
to Circos
Any updates on these issues.
make-table -row 3 -seed 123 -brief > samples/table.txt : table is empty.
Copied table from example: parse-example-1.txt
-,A,B,C
A,0,1,2
B,3,4,5
C,6,7,8

cat samples/ parse-example-1 .txt | make-conf -dir data
Illegal division by zero at /home/shree/anaconda3/envs/Circos_tools/bin/parse-table line 664, <FILE> line 6.

Any help would be really would be really nice and appreciated.
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