File Not Found error: File (...) /.causal.txt' does not exist"

[silvenchu]

Hello,

I'm running the code using the example input GR018. I cloned the repo, set up conda environment and download fine-mapping tools and build the reference panel without errors. However, after running:

python fine_map_pipe.py -s 120575 ./input/GR018.txt.gz output

I foun the following error:

"FileNotFoundError: File b'/git/CAUSALdb-finemapping-pip/GR018/GR018_1_54226262_56413117.causal.txt' does not exist"

Could you help please?

[Jianhua-Wang]

Did you activate the conda environment before you ran the command?

[silvenchu]

Hello Jianhua,

Thank you very much for your response!

Yes, I activate the environment. My version of conda is 4.11. These are my commands using the latest version of the environment:

conda env create -f /home/lab022/WORK/Silvia/credset/CAUSALdb-finemapping-pip/bin/finemapcondaenv.yml

conda activate finemap

python3 fine_map_pipe.py -s 120575 ./input/GR018.txt.gz output

After running the third command I got the following error:

loading input file
split files
prepare input files of finemapping tools
run finemapping tools
gather results
Traceback (most recent call last):
File "fine_map_pipe.py", line 286, in
get_credible_set(prefix)
File "fine_map_pipe.py", line 130, in get_credible_set
df = pd.read_csv(f'{out_dir}/{meta_id}{chr_id}{start}_{stop}.causal.txt',sep='\t',names=names)
File "/home/lab022/anaconda3/envs/finemap/lib/python3.6/site-packages/pandas/io/parsers.py", line 705, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/lab022/anaconda3/envs/finemap/lib/python3.6/site-packages/pandas/io/parsers.py", line 445, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/lab022/anaconda3/envs/finemap/lib/python3.6/site-packages/pandas/io/parsers.py", line 814, in init
self._make_engine(self.engine)
File "/home/lab022/anaconda3/envs/finemap/lib/python3.6/site-packages/pandas/io/parsers.py", line 1045, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/home/lab022/anaconda3/envs/finemap/lib/python3.6/site-packages/pandas/io/parsers.py", line 1684, in init
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 391, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 710, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: File b'/home/lab022/WORK/Silvia/credset/CAUSALdb-finemapping-pip/GR018/GR018_1_54226262_56413117.causal.txt' does not exist

This is how the input file looks like:
(finemap) lab022@PCIR1184:~/WORK/Silvia/credset/CAUSALdb-finemapping-pip/input$ head GR018.txt CHR BP rsID MAF EA NEA BETA SE P Zscore
1 762320 exm2268640 C T -2.1671804559878427 2.2192489884814903 0.3288 -0.9765377689642318
1 865584 exm44 G A -0.7989522394569218 0.9458814406017895 0.3983 -0.844664251947487
1 865625 exm46 G A -1.723727058836228 1.3810903732349589 0.212 -1.2480914299610266
1 865628 exm47 A G -3.798694320121143 11.010921607693835 0.7301 -0.34499331259127497
1 865662 exm51 G A -1.6841614586300369 1.0159911755963904 0.09739 -1.657653628380609
1 865665 exm53 G A -2.0091694886945044 2.640410901770726 0.4467 -0.7609306139991715
1 865694 exm55 C T -1.0624732420522365 0.4776340446018991 0.02612 -2.2244504010131694
1 866438 exm63 G A -0.8360941898798784 1.1243371703006841 0.4571 -0.7436329705761482
1 874501 exm94 C T -2.6664285264113907 8.142085007626491 0.7433 -0.32748718834473145

Do you know what can be going wrong? Thanks a lot!!

[ZJ-zuojing]

Hello silvenchu，
I also have the same question,Did you solve it?
@silvenchu thank you !

[xiechengyong123]

Me too!
@silvenchu thank you !

[Jianhua-Wang]

hey guys, I found this pipeline is less portable. Now I am working on a new pipeline along with some new features, such as custom LD reference panel and block window size. Please wait patiently.

[silvenchu]

Hello @xiechengyong123 !

We were able to run the code after making some changes. The path were some files were stored was wrong and that's why they couldn't be found. I am attaching our modified code:

fine_map_pipe_natalia.pdf

[xiechengyong123]

silvenchu Hello! I have received your email. I admire your spirit of selfless code sharing. Feel free to contact and communicate with me if you have any questions, good luck! 2022-7-18 | | 谢成勇 | | ***@***.*** | ---- Replied Message ---- | From | ***@***.***> | | Date | 7/15/2022 23:02 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [mulinlab/CAUSALdb-finemapping-pip] File Not Found error: File (...) /.causal.txt' does not exist" (Issue #9) | Hello @xiechengyong123 ! We were able to run the code after making some changes. The path were some files were stored was wrong and that's why they couldn't be found. I am attaching our modified code: fine_map_pipe_natalia.pdf — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[silvenchu]

@xiechengyong123 Sure! :) Credits go to my colleague Natalia Llonga, she modified the code and it worked, hope you managed to make it work too!

silvenchu Hello! I have received your email. I admire your spirit of selfless code sharing. Feel free to contact and communicate with me if you have any questions, good luck! 2022-7-18 | | 谢成勇 | | @.*** | ---- Replied Message ---- | From | @.> | | Date | 7/15/2022 23:02 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [mulinlab/CAUSALdb-finemapping-pip] File Not Found error: File (...) /.causal.txt' does not exist" (Issue #9) | Hello @xiechengyong123 ! We were able to run the code after making some changes. The path were some files were stored was wrong and that's why they couldn't be found. I am attaching our modified code: fine_map_pipe_natalia.pdf — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[liggettla]

I went through the code, and it looks like when rsID is left as NA or anything repetitive, all data will be dropped, producing the missing *causal.txt error. Instead of removing duplicates within the rsID column, duplicates can be removed on the 'CHR','BP','EA','NEA' columns, and allows everything to run even with an absent rsID.

The following changes to the code should work:

54     # processed['rsID'] = processed['ID'] # makes rsID column all the same data
55     # processed = processed.drop_duplicates('rsID') # if rsID is blank, all data is removed
56     processed = processed.drop_duplicates(['CHR','BP','EA','NEA']) # instead drop on location

[shudanhua]

I went through the code, and it looks like when rsID is left as NA or anything repetitive, all data will be dropped, producing the missing *causal.txt error. Instead of removing duplicates within the rsID column, duplicates can be removed on the 'CHR','BP','EA','NEA' columns, and allows everything to run even with an absent rsID.

The following changes to the code should work:

54     # processed['rsID'] = processed['ID'] # makes rsID column all the same data
55     # processed = processed.drop_duplicates('rsID') # if rsID is blank, all data is removed
56     processed = processed.drop_duplicates(['CHR','BP','EA','NEA']) # instead drop on location

Thank you so much! It worked!

[yunaibiao]

Hello @xiechengyong123 ! 你好 ！

We were able to run the code after making some changes. The path were some files were stored was wrong and that's why they couldn't be found. I am attaching our modified code:进行一些更改后，我们能够运行代码。有些文件存储的路径错误，导致找不到。我附上我们修改后的代码：

fine_map_pipe_natalia.pdf

hello,Could you provide the .py file?