fengcong3 / happe Goto Github PK

HAPPE keeps complaining "no such file or directory" but weirdly it is complaining about how it cannot find the OUTPUT file that would be created when I provide the --output argument

Here's the error using your example files. I'm on a Mac running 13.5.2 and using zsh as my shell (although I tried in bash too).

% HAPPE \
-g happe.config \
-v SEVIR.592.SNP.ann.allele2.part.vcf.gz \
-i sample_inf.tsv \
-c sample.color.txt \
-k small_example.list \
-o SEVIR_5G085400v2

[2023-10-02 16:31:25,816] - HAPPE - INFO - deal args.
[2023-10-02 16:31:25,818] - HAPPE - INFO - Filter samples and variants.
ln: SEVIR_5G085400v2.vcf.gz: No such file or directory
[2023-10-02 16:31:25,842] - HAPPE - ERROR - Filter samples and variants. -- retrun code:256

Hello,

I tried to run the script on test data and I get an error linked to the execution of pheat2excel_V5.py.
You can find the error log down below.
I would also like to know if it is possible to have access to your publication data to be sure that any problem is not data related.

Best regards,
Abdel

****Traceback (most recent call last):  File "/home/s953680/apps/python/current/lib/python3.8/site-packages/openpyxl-3.2.0b1-py3.8.egg/openpyxl/utils/cell.py", line 110, in get_column_letter    return _STRING_COL_CACHE[idx]
KeyError: 18279

During handling of the above exception, another exception occurred:

Traceback (most recent call last):  File "/home/s953680/apps/python/3.8/lib/python3.8/site-packages/HAPPE-0.1.4-py3.8.egg/HAPPE/pheat2excel_V5.py", line 225, in     col_let = get_column_letter(start_col+index+2)  File "/home/s953680/apps/python/current/lib/python3.8/site-packages/openpyxl-3.2.0b1-py3.8.egg/openpyxl/utils/cell.py", line 112, in get_column_letter    raise ValueError("Invalid column index {0}".format(idx))
ValueError: Invalid column index 18279
[2022-09-06 16:29:36,947] - HAPPE - ERROR - add heat matrix -- retrun code:256
like 1****

Hi there,

I'm trying to run HAPPE on my test dataset, but I am encountering this issue.

Thanks very much in advance for the help!

Mikal

Hello,
I am trying to install and use your program but I cannot find the file excel_haplotype.py.
It is referenced in the init_.py script and I get an error when trying to install it.
Then when I do replace from .excel_haplotype import main_1, the program stops at a clustering step.
Would you please help me with that ?
Best regards,
Abdel

Dear HAPPE Team:

I got the error as below, May you give me some suggestion? Thank you so much

(Python3_6) HAPPE -v 2023NKSC_F1reseq_allele2_maf0.05_DP20_missing0.9.recode.vcf.gz -g config.ini -c NKSCsample.color -i NKSCsample_inf.tsv -o ./HAPPE
[2023-03-06 21:11:02,529] - HAPPE - INFO - deal args.
[2023-03-06 21:11:02,529] - HAPPE - INFO - Filter samples and variants.
[2023-03-06 21:11:02,531] - HAPPE - INFO - convert file format.
[2023-03-06 21:11:04,243] - HAPPE - INFO - hierarchy clustering.
cluster min and max: 1 29
[2023-03-06 21:11:06,848] - HAPPE - INFO - read snp information file.
[2023-03-06 21:11:06,848] - HAPPE - INFO - calc out the snp_info_row_num = 7.
[2023-03-06 21:11:06,848] - HAPPE - INFO - plot tree to excel file.
[2023-03-06 21:11:09,489] - HAPPE - INFO - get sample information start col and get sample order.
[2023-03-06 21:11:09,496] - HAPPE - INFO - write sample information to excel file.
Traceback (most recent call last):
File "/home/hsiang/miniconda3/envs/Python3_6/lib/python3.6/site-packages/HAPPE/sampleinf2excel_V2.py", line 97, in
color_fill = PatternFill(fgColor=color_d[sample], fill_type="solid")
KeyError: '6_9'
[2023-03-06 21:11:10,120] - HAPPE - ERROR - write sample information to excel file -- retrun code:256