unboundlocalerror local variable 'f' referenced before assignment

Local variable referenced before assignment in Python

Last updated: Apr 8, 2024 Reading time · 4 min

# Local variable referenced before assignment in Python

The Python "UnboundLocalError: Local variable referenced before assignment" occurs when we reference a local variable before assigning a value to it in a function.

To solve the error, mark the variable as global in the function definition, e.g. global my_var .

Here is an example of how the error occurs.

We assign a value to the name variable in the function.

# Mark the variable as global to solve the error

To solve the error, mark the variable as global in your function definition.

If a variable is assigned a value in a function's body, it is a local variable unless explicitly declared as global .

# Local variables shadow global ones with the same name

You could reference the global name variable from inside the function but if you assign a value to the variable in the function's body, the local variable shadows the global one.

Accessing the name variable in the function is perfectly fine.

On the other hand, variables declared in a function cannot be accessed from the global scope.

The name variable is declared in the function, so trying to access it from outside causes an error.

Make sure you don't try to access the variable before using the global keyword, otherwise, you'd get the SyntaxError: name 'X' is used prior to global declaration error.

# Returning a value from the function instead

An alternative solution to using the global keyword is to return a value from the function and use the value to reassign the global variable.

We simply return the value that we eventually use to assign to the name global variable.

# Passing the global variable as an argument to the function

You should also consider passing the global variable as an argument to the function.

We passed the name global variable as an argument to the function.

If we assign a value to a variable in a function, the variable is assumed to be local unless explicitly declared as global .

# Assigning a value to a local variable from an outer scope

If you have a nested function and are trying to assign a value to the local variables from the outer function, use the nonlocal keyword.

The nonlocal keyword allows us to work with the local variables of enclosing functions.

Had we not used the nonlocal statement, the call to the print() function would have returned an empty string.

Printing the message variable on the last line of the function shows an empty string because the inner() function has its own scope.

Changing the value of the variable in the inner scope is not possible unless we use the nonlocal keyword.

Instead, the message variable in the inner function simply shadows the variable with the same name from the outer scope.

# Discussion

As shown in this section of the documentation, when you assign a value to a variable inside a function, the variable:

• Becomes local to the scope.
• Shadows any variables from the outer scope that have the same name.

The last line in the example function assigns a value to the name variable, marking it as a local variable and shadowing the name variable from the outer scope.

At the time the print(name) line runs, the name variable is not yet initialized, which causes the error.

The most intuitive way to solve the error is to use the global keyword.

The global keyword is used to indicate to Python that we are actually modifying the value of the name variable from the outer scope.

• If a variable is only referenced inside a function, it is implicitly global.
• If a variable is assigned a value inside a function's body, it is assumed to be local, unless explicitly marked as global .

If you want to read more about why this error occurs, check out [this section] ( this section ) of the docs.

# Additional Resources

You can learn more about the related topics by checking out the following tutorials:

• SyntaxError: name 'X' is used prior to global declaration

Borislav Hadzhiev

Web Developer

Copyright © 2024 Borislav Hadzhiev

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UnboundLocalError Local variable Referenced Before Assignment in Python

Handling errors is an integral part of writing robust and reliable Python code. One common stumbling block that developers often encounter is the “UnboundLocalError” raised within a try-except block. This error can be perplexing for those unfamiliar with its nuances but fear not – in this article, we will delve into the intricacies of the UnboundLocalError and provide a comprehensive guide on how to effectively use try-except statements to resolve it.

What is UnboundLocalError Local variable Referenced Before Assignment in Python?

The UnboundLocalError occurs when a local variable is referenced before it has been assigned a value within a function or method. This error typically surfaces when utilizing try-except blocks to handle exceptions, creating a puzzle for developers trying to comprehend its origins and find a solution.

Why does UnboundLocalError: Local variable Referenced Before Assignment Occur?

below, are the reasons of occurring “Unboundlocalerror: Try Except Statements” in Python :

Variable Assignment Inside Try Block

Reassigning a global variable inside except block.

• Accessing a Variable Defined Inside an If Block

In the below code, example_function attempts to execute some_operation within a try-except block. If an exception occurs, it prints an error message. However, if no exception occurs, it prints the value of the variable result outside the try block, leading to an UnboundLocalError since result might not be defined if an exception was caught.

In below code , modify_global function attempts to increment the global variable global_var within a try block, but it raises an UnboundLocalError. This error occurs because the function treats global_var as a local variable due to the assignment operation within the try block.

Solution for UnboundLocalError Local variable Referenced Before Assignment

Below, are the approaches to solve “Unboundlocalerror: Try Except Statements”.

Initialize Variables Outside the Try Block

Avoid reassignment of global variables.

In modification to the example_function is correct. Initializing the variable result before the try block ensures that it exists even if an exception occurs within the try block. This helps prevent UnboundLocalError when trying to access result in the print statement outside the try block.

Below, code calculates a new value ( local_var ) based on the global variable and then prints both the local and global variables separately. It demonstrates that the global variable is accessed directly without being reassigned within the function.

In conclusion , To fix “UnboundLocalError” related to try-except statements, ensure that variables used within the try block are initialized before the try block starts. This can be achieved by declaring the variables with default values or assigning them None outside the try block. Additionally, when modifying global variables within a try block, use the `global` keyword to explicitly declare them.

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How to fix UnboundLocalError: local variable 'x' referenced before assignment in Python

by Nathan Sebhastian

Posted on May 26, 2023

Reading time: 2 minutes

One error you might encounter when running Python code is:

This error commonly occurs when you reference a variable inside a function without first assigning it a value.

You could also see this error when you forget to pass the variable as an argument to your function.

Let me show you an example that causes this error and how I fix it in practice.

How to reproduce this error

Suppose you have a variable called name declared in your Python code as follows:

Next, you created a function that uses the name variable as shown below:

When you execute the code above, you’ll get this error:

This error occurs because you both assign and reference a variable called name inside the function.

Python thinks you’re trying to assign the local variable name to name , which is not the case here because the original name variable we declared is a global variable.

How to fix this error

To resolve this error, you can change the variable’s name inside the function to something else. For example, name_with_title should work:

As an alternative, you can specify a name parameter in the greet() function to indicate that you require a variable to be passed to the function.

When calling the function, you need to pass a variable as follows:

This code allows Python to know that you intend to use the name variable which is passed as an argument to the function as part of the newly declared name variable.

Still, I would say that you need to use a different name when declaring a variable inside the function. Using the same name might confuse you in the future.

Here’s the best solution to the error:

Now it’s clear that we’re using the name variable given to the function as part of the value assigned to name_with_title . Way to go!

The UnboundLocalError: local variable 'x' referenced before assignment occurs when you reference a variable inside a function before declaring that variable.

To resolve this error, you need to use a different variable name when referencing the existing variable, or you can also specify a parameter for the function.

I hope this tutorial is useful. See you in other tutorials.

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Python local variable referenced before assignment Solution

When you start introducing functions into your code, you’re bound to encounter an UnboundLocalError at some point. This error is raised when you try to use a variable before it has been assigned in the local context .

In this guide, we talk about what this error means and why it is raised. We walk through an example of this error in action to help you understand how you can solve it.

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What is unboundlocalerror: local variable referenced before assignment.

Trying to assign a value to a variable that does not have local scope can result in this error:

Python has a simple rule to determine the scope of a variable. If a variable is assigned in a function , that variable is local. This is because it is assumed that when you define a variable inside a function you only need to access it inside that function.

There are two variable scopes in Python: local and global. Global variables are accessible throughout an entire program; local variables are only accessible within the function in which they are originally defined.

Let’s take a look at how to solve this error.

An Example Scenario

We’re going to write a program that calculates the grade a student has earned in class.

We start by declaring two variables:

These variables store the numerical and letter grades a student has earned, respectively. By default, the value of “letter” is “F”. Next, we write a function that calculates a student’s letter grade based on their numerical grade using an “if” statement :

Finally, we call our function:

This line of code prints out the value returned by the calculate_grade() function to the console. We pass through one parameter into our function: numerical. This is the numerical value of the grade a student has earned.

Let’s run our code and see what happens:

An error has been raised.

The Solution

Our code returns an error because we reference “letter” before we assign it.

We have set the value of “numerical” to 42. Our if statement does not set a value for any grade over 50. This means that when we call our calculate_grade() function, our return statement does not know the value to which we are referring.

We do define “letter” at the start of our program. However, we define it in the global context. Python treats “return letter” as trying to return a local variable called “letter”, not a global variable.

We solve this problem in two ways. First, we can add an else statement to our code. This ensures we declare “letter” before we try to return it:

Let’s try to run our code again:

Our code successfully prints out the student’s grade.

If you are using an “if” statement where you declare a variable, you should make sure there is an “else” statement in place. This will make sure that even if none of your if statements evaluate to True, you can still set a value for the variable with which you are going to work.

Alternatively, we could use the “global” keyword to make our global keyword available in the local context in our calculate_grade() function. However, this approach is likely to lead to more confusing code and other issues. In general, variables should not be declared using “global” unless absolutely necessary . Your first, and main, port of call should always be to make sure that a variable is correctly defined.

In the example above, for instance, we did not check that the variable “letter” was defined in all use cases.

That’s it! We have fixed the local variable error in our code.

The UnboundLocalError: local variable referenced before assignment error is raised when you try to assign a value to a local variable before it has been declared. You can solve this error by ensuring that a local variable is declared before you assign it a value.

Now you’re ready to solve UnboundLocalError Python errors like a professional developer !

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[SOLVED] Local Variable Referenced Before Assignment

Python treats variables referenced only inside a function as global variables. Any variable assigned to a function’s body is assumed to be a local variable unless explicitly declared as global.

Why Does This Error Occur?

Unboundlocalerror: local variable referenced before assignment occurs when a variable is used before its created. Python does not have the concept of variable declarations. Hence it searches for the variable whenever used. When not found, it throws the error.

Before we hop into the solutions, let’s have a look at what is the global and local variables.

Local Variable Declarations vs. Global Variable Declarations

Local Variable Referenced Before Assignment Error with Explanation

Try these examples yourself using our Online Compiler.

Let’s look at the following function:

Explanation

The variable myVar has been assigned a value twice. Once before the declaration of myFunction and within myFunction itself.

Using Global Variables

Passing the variable as global allows the function to recognize the variable outside the function.

Create Functions that Take in Parameters

Instead of initializing myVar as a global or local variable, it can be passed to the function as a parameter. This removes the need to create a variable in memory.

UnboundLocalError: local variable ‘DISTRO_NAME’

This error may occur when trying to launch the Anaconda Navigator in Linux Systems.

Upon launching Anaconda Navigator, the opening screen freezes and doesn’t proceed to load.

Try and update your Anaconda Navigator with the following command.

If solution one doesn’t work, you have to edit a file located at

After finding and opening the Python file, make the following changes:

In the function on line 159, simply add the line:

DISTRO_NAME = None

Save the file and re-launch Anaconda Navigator.

DJANGO – Local Variable Referenced Before Assignment [Form]

The program takes information from a form filled out by a user. Accordingly, an email is sent using the information.

Upon running you get the following error:

We have created a class myForm that creates instances of Django forms. It extracts the user’s name, email, and message to be sent.

A function GetContact is created to use the information from the Django form and produce an email. It takes one request parameter. Prior to sending the email, the function verifies the validity of the form. Upon True , .get() function is passed to fetch the name, email, and message. Finally, the email sent via the send_mail function

Why does the error occur?

We are initializing form under the if request.method == “POST” condition statement. Using the GET request, our variable form doesn’t get defined.

Local variable Referenced before assignment but it is global

This is a common error that happens when we don’t provide a value to a variable and reference it. This can happen with local variables. Global variables can’t be assigned.

This error message is raised when a variable is referenced before it has been assigned a value within the local scope of a function, even though it is a global variable.

Here’s an example to help illustrate the problem:

In this example, x is a global variable that is defined outside of the function my_func(). However, when we try to print the value of x inside the function, we get a UnboundLocalError with the message “local variable ‘x’ referenced before assignment”.

This is because the += operator implicitly creates a local variable within the function’s scope, which shadows the global variable of the same name. Since we’re trying to access the value of x before it’s been assigned a value within the local scope, the interpreter raises an error.

To fix this, you can use the global keyword to explicitly refer to the global variable within the function’s scope:

However, in the above example, the global keyword tells Python that we want to modify the value of the global variable x, rather than creating a new local variable. This allows us to access and modify the global variable within the function’s scope, without causing any errors.

Local variable ‘version’ referenced before assignment ubuntu-drivers

This error occurs with Ubuntu version drivers. To solve this error, you can re-specify the version information and give a split as 2 –

Here, p_name means package name.

With the help of the threading module, you can avoid using global variables in multi-threading. Make sure you lock and release your threads correctly to avoid the race condition.

When a variable that is created locally is called before assigning, it results in Unbound Local Error in Python. The interpreter can’t track the variable.

Therefore, we have examined the local variable referenced before the assignment Exception in Python. The differences between a local and global variable declaration have been explained, and multiple solutions regarding the issue have been provided.

Trending Python Articles

Python UnboundLocalError: local variable referenced before assignment

by Suf | Programming , Python , Tips

If you try to reference a local variable before assigning a value to it within the body of a function, you will encounter the UnboundLocalError: local variable referenced before assignment.

The preferable way to solve this error is to pass parameters to your function, for example:

Alternatively, you can declare the variable as global to access it while inside a function. For example,

This tutorial will go through the error in detail and how to solve it with code examples .

Table of contents

What is scope in python, unboundlocalerror: local variable referenced before assignment, solution #1: passing parameters to the function, solution #2: use global keyword, solution #1: include else statement, solution #2: use global keyword.

Scope refers to a variable being only available inside the region where it was created. A variable created inside a function belongs to the local scope of that function, and we can only use that variable inside that function.

A variable created in the main body of the Python code is a global variable and belongs to the global scope. Global variables are available within any scope, global and local.

UnboundLocalError occurs when we try to modify a variable defined as local before creating it. If we only need to read a variable within a function, we can do so without using the global keyword. Consider the following example that demonstrates a variable var created with global scope and accessed from test_func :

If we try to assign a value to var within test_func , the Python interpreter will raise the UnboundLocalError:

This error occurs because when we make an assignment to a variable in a scope, that variable becomes local to that scope and overrides any variable with the same name in the global or outer scope.

var +=1 is similar to var = var + 1 , therefore the Python interpreter should first read var , perform the addition and assign the value back to var .

var is a variable local to test_func , so the variable is read or referenced before we have assigned it. As a result, the Python interpreter raises the UnboundLocalError.

Example #1: Accessing a Local Variable

Let’s look at an example where we define a global variable number. We will use the increment_func to increase the numerical value of number by 1.

Let’s run the code to see what happens:

The error occurs because we tried to read a local variable before assigning a value to it.

We can solve this error by passing a parameter to increment_func . This solution is the preferred approach. Typically Python developers avoid declaring global variables unless they are necessary. Let’s look at the revised code:

We have assigned a value to number and passed it to the increment_func , which will resolve the UnboundLocalError. Let’s run the code to see the result:

We successfully printed the value to the console.

We also can solve this error by using the global keyword. The global statement tells the Python interpreter that inside increment_func , the variable number is a global variable even if we assign to it in increment_func . Let’s look at the revised code:

Let’s run the code to see the result:

Example #2: Function with if-elif statements

Let’s look at an example where we collect a score from a player of a game to rank their level of expertise. The variable we will use is called score and the calculate_level function takes in score as a parameter and returns a string containing the player’s level .

In the above code, we have a series of if-elif statements for assigning a string to the level variable. Let’s run the code to see what happens:

The error occurs because we input a score equal to 40 . The conditional statements in the function do not account for a value below 55 , therefore when we call the calculate_level function, Python will attempt to return level without any value assigned to it.

We can solve this error by completing the set of conditions with an else statement. The else statement will provide an assignment to level for all scores lower than 55 . Let’s look at the revised code:

In the above code, all scores below 55 are given the beginner level. Let’s run the code to see what happens:

We can also create a global variable level and then use the global keyword inside calculate_level . Using the global keyword will ensure that the variable is available in the local scope of the calculate_level function. Let’s look at the revised code.

In the above code, we put the global statement inside the function and at the beginning. Note that the “default” value of level is beginner and we do not include the else statement in the function. Let’s run the code to see the result:

Congratulations on reading to the end of this tutorial! The UnboundLocalError: local variable referenced before assignment occurs when you try to reference a local variable before assigning a value to it. Preferably, you can solve this error by passing parameters to your function. Alternatively, you can use the global keyword.

If you have if-elif statements in your code where you assign a value to a local variable and do not account for all outcomes, you may encounter this error. In which case, you must include an else statement to account for the missing outcome.

For further reading on Python code blocks and structure, go to the article: How to Solve Python IndentationError: unindent does not match any outer indentation level .

Go to the  online courses page on Python  to learn more about Python for data science and machine learning.

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Fix "local variable referenced before assignment" in Python

Introduction

If you're a Python developer, you've probably come across a variety of errors, like the "local variable referenced before assignment" error. This error can be a bit puzzling, especially for beginners and when it involves local/global variables.

Today, we'll explain this error, understand why it occurs, and see how you can fix it.

The "local variable referenced before assignment" Error

The "local variable referenced before assignment" error in Python is a common error that occurs when a local variable is referenced before it has been assigned a value. This error is a type of UnboundLocalError , which is raised when a local variable is referenced before it has been assigned in the local scope.

Here's a simple example:

Running this code will throw the "local variable 'x' referenced before assignment" error. This is because the variable x is referenced in the print(x) statement before it is assigned a value in the local scope of the foo function.

Even more confusing is when it involves global variables. For example, the following code also produces the error:

But wait, why does this also produce the error? Isn't x assigned before it's used in the say_hello function? The problem here is that x is a global variable when assigned "Hello ". However, in the say_hello function, it's a different local variable, which has not yet been assigned.

We'll see later in this Byte how you can fix these cases as well.

Fixing the Error: Initialization

One way to fix this error is to initialize the variable before using it. This ensures that the variable exists in the local scope before it is referenced.

Let's correct the error from our first example:

In this revised code, we initialize x with a value of 1 before printing it. Now, when you run the function, it will print 1 without any errors.

Fixing the Error: Global Keyword

Another way to fix this error, depending on your specific scenario, is by using the global keyword. This is especially useful when you want to use a global variable inside a function.

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Here's how:

In this snippet, we declare x as a global variable inside the function foo . This tells Python to look for x in the global scope, not the local one . Now, when you run the function, it will increment the global x by 1 and print 1 .

Similar Error: NameError

An error that's similar to the "local variable referenced before assignment" error is the NameError . This is raised when you try to use a variable or a function name that has not been defined yet.

Running this code will result in a NameError :

In this case, we're trying to print the value of y , but y has not been defined anywhere in the code. Hence, Python raises a NameError . This is similar in that we are trying to use an uninitialized/undefined variable, but the main difference is that we didn't try to initialize y anywhere else in our code.

Variable Scope in Python

Understanding the concept of variable scope can help avoid many common errors in Python, including the main error of interest in this Byte. But what exactly is variable scope?

In Python, variables have two types of scope - global and local. A variable declared inside a function is known as a local variable, while a variable declared outside a function is a global variable.

Consider this example:

In this code, x is a global variable, and y is a local variable. x can be accessed anywhere in the code, but y can only be accessed within my_function . Confusion surrounding this is one of the most common causes for the "variable referenced before assignment" error.

In this Byte, we've taken a look at the "local variable referenced before assignment" error and another similar error, NameError . We also delved into the concept of variable scope in Python, which is an important concept to understand to avoid these errors. If you're seeing one of these errors, check the scope of your variables and make sure they're being assigned before they're being used.

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How to Fix Local Variable Referenced Before Assignment Error in Python

Table of Contents

Fixing local variable referenced before assignment error.

In Python , when you try to reference a variable that hasn't yet been given a value (assigned), it will throw an error.

That error will look like this:

In this post, we'll see examples of what causes this and how to fix it.

Let's begin by looking at an example of this error:

If you run this code, you'll get

The issue is that in this line:

We are defining a local variable called value and then trying to use it before it has been assigned a value, instead of using the variable that we defined in the first line.

If we want to refer the variable that was defined in the first line, we can make use of the global keyword.

The global keyword is used to refer to a variable that is defined outside of a function.

Let's look at how using global can fix our issue here:

Global variables have global scope, so you can referenced them anywhere in your code, thus avoiding the error.

If you run this code, you'll get this output:

In this post, we learned at how to avoid the local variable referenced before assignment error in Python.

The error stems from trying to refer to a variable without an assigned value, so either make use of a global variable using the global keyword, or assign the variable a value before using it.

Thanks for reading!

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What is UnboundLocalError: local variable referenced before assignment?

Trying to assign a value to a variable that does not have local scope can result in this error:

Python has a simple rule to determine the scope of a variable. To clarify, a variable is assigned in a function, that variable is local. Because it is assumed that when you define a variable inside a function, you only need to access it inside that function.

There are two variable scopes in Python: local and global. Global variables are accessible throughout an entire program. Whereas, local variables are only accessible within the function in which they are originally defined.

An example of Local variable referenced before assignment

We’re going to write a program that calculates the grade a student has earned in class.

Firstly, we start by declaring two variables:

These variables store the numerical and letter grades a student has earned, respectively. By default, the value of “letter” is “F”. Then, we write a function that calculates a student’s letter grade based on their numerical grade using an “if” statement:

Finally, we call our function:

This line of code prints out the value returned by the  calculate_grade()  function to the console. We pass through one parameter into our function: numerical. This is the numerical value of the grade a student has earned.

Let’s run our code of Local variable referenced before assignment and see what happens:

Here is an error!

The Solution of Local variable referenced before assignment

The code returns an error: Unboundlocalerror local variable referenced before assignment because we reference “letter” before we assign it.

We have set the value of “numerical” to 42. Our  if  statement does not set a value for any grade over 50. This means that when we call our  calculate_grade()  function, our return statement does not know the value to which we are referring.

Moreover, we do define “letter” at the start of our program. However, we define it in the global context. Because Python treats “return letter” as trying to return a local variable called “letter”, not a global variable.

Therefore, this problem of variable referenced before assignment could be solved in two ways. Firstly, we can add an  else  statement to our code. This ensures we declare “letter” before we try to return it:

Let’s try to run our code again:

Our code successfully prints out the student’s grade. This approach is good because it lets us keep “letter” in the local context. To clarify, we could even remove the “letter = “F”” statement from the top of our code because we do not use it in the global context.

Alternatively, we could use the “global” keyword to make our global keyword available in the local context in our  calculate_grade()  function:

We use the “global” keyword at the start of our function.

This keyword changes the scope of our variable to a global variable. This means the “return” statement will no longer treat “letter” like a local variable. Let’s run our code. Our code returns: F.

The code works successfully! Let’s try it using a different grade number by setting the value of “numerical” to a new number:

Our code returns: B.

Finally, we have fixed the local variable referenced before assignment error in the code.

To sum up, as you can see, the UnboundLocalError: local variable referenced before assignment error is raised when you try to assign a value to a local variable before it has been declared. Then, you can solve this error by ensuring that a local variable is declared before you assign it a value. Moreover, if a variable is declared globally that you want to access in a function, you can use the “global” keyword to change its value. In case you have any inquiry, let’s CONTACT US . With a lot of experience in Mobile app development services , we will surely solve it for you instantly.

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Metaphlan3 running problem UnboundLocalError

I had an error when running metaphlan3 in the first step. My command is “metaphlan SRR7563636_1.fastq,SRR7563636_2.fastq --input_type fastq -s sams/SRR7563636.sam.bz2 --bowtie2out bowtie2/SRR7563636.bowtie2.bz2 -o profiles/SRR7563636_profile.tsv”.

But it reported, Downloading https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1

Warning: Unable to download https://www.dropbox.com/sh/7qze7m7g9fe2xjg/AAA4XDP85WHon_eHvztxkamTa/file_list.txt?dl=1 Traceback (most recent call last): File “/gpfs/share/apps/python/cpu/3.6.5/bin/metaphlan”, line 8, in sys.exit(main()) File “/gpfs/share/apps/python/cpu/3.6.5/lib/python3.6/site-packages/metaphlan/metaphlan.py”, line 916, in main pars[‘index’] = check_and_install_database(pars[‘index’], pars[‘bowtie2db’], pars[‘bowtie2_build’], pars[‘nproc’], pars[‘force_download’]) File “/gpfs/share/apps/python/cpu/3.6.5/lib/python3.6/site-packages/metaphlan/init.py”, line 271, in check_and_install_database index = resolve_latest_database(bowtie2_db, ls_f[‘mpa_latest’], force_redownload_latest) UnboundLocalError: local variable ‘ls_f’ referenced before assignment

I can’t download the database by dropbox on our public server. Is there any way to solve or bypass this problem? For example, could I download the file and deposit it under some directory? Thank you so much!

Yes, you can download the database from Zenodo https://zenodo.org/record/3957592#.XzYjcB7RZ-E

and run MetaPhlan with the -x mpa_v30_CHOCOPhlAn_201901 parameter. You probably should update your installation, the latest version (3.0.2) automatically retrieves the database from Zenodo if Dropbox fails.

Thank you so much!!! I will try it.

Hi, Sorry to bother you. I download the database and deposited it under the path “/gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901”. I have tried to specify the database by using

• “metaphlan SRR7563636_1.fastq,SRR7563636_2.fastq --input_type fastq -s sams/SRR7563636.sam.bz2 –bowtie2db /gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901 -x mpa_v30_CHOCOPhlAn_201901 --bowtie2out bowtie2/SRR7563636.bowtie2.bz2 -o profiles/SRR7563636_profile.tsv”
• “metaphlan SRR7563636_1.fastq,SRR7563636_2.fastq --input_type fastq -s sams/SRR7563636.sam.bz2 -x mpa_v30_CHOCOPhlAn_201901 --bowtie2out bowtie2/SRR7563636.bowtie2.bz2 -o profiles/SRR7563636_profile.tsv”
• “metaphlan SRR7563636_1.fastq,SRR7563636_2.fastq --input_type fastq -s sams/SRR7563636.sam.bz2 –bowtie2db /gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901 --bowtie2out bowtie2/SRR7563636.bowtie2.bz2 -o profiles/SRR7563636_profile.tsv”

However, none of these commands worked. The tutorial just said, “Just download the .tar, .md5, and the mpa_latest files and place them in the metaphlan_databases folder .” So, where should I deposit the database? How can I let the metaphlan know where to find the database? Thank you so much!

Have you built the database with bowtie2-build ?

Yes, I have built the database under “/gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901” and obtained “mpa_v30_CHOCOPhlAn_201901.1.bt2”. But when I ran “metaphlan SRR7563636_1.fastq,SRR7563636_2.fastq --input_type fastq -s sams/SRR7563636.sam.bz2 –bowtie2db /gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901 --index mpa_v30_CHOCOPhlAn_201901 --bowtie2out bowtie2/SRR7563636.bowtie2.bz2 -o profiles/SRR7563636_profile.tsv”, it still reported the following error.

Downloading … Warning: Unable to download No MetaPhlAn BowTie2 database found (–index option)! Expecting location /gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901/mpa_v30_CHOCOPhlAn_201901 Exiting…

Due to some internet safety issues, the metaphlan can’t automatically download the database. So where should I deposit the built database? How should I name the folder that contains the database? Thank you so much for your kindly help!

Is it the only file you got? You should have six .bt2 files in the “/gpfs/data/lilab/home/zhoub03/software/metaphlan3_database/mpa_v30_CHOCOPhlAn_201901” folder

Thank you so much! The bowtie reference was not completely generated. Now, this problem has been solved.

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UnboundLocalError: local variable 'pdf' referenced before assignment #172

awalker4 commented Aug 1, 2023 • edited

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