Open moOsmanMD opened 12 months ago
This seems a format issue. Could you show the value of f_in? It seems no file provided? In addition, which line f line in f_in
locates?
Thanks a lot for your response
this is the output I get
[2023-09-08 15:29:32,726] INFO Monopogen.py Performing data preprocess before variant calling...
[2023-09-08 15:29:32,726] INFO germline.py Parameters in effect:
[2023-09-08 15:29:32,726] INFO germline.py --subcommand = [preProcess]
[2023-09-08 15:29:32,726] INFO germline.py --bamFile = [example/A.bam]
[2023-09-08 15:29:32,726] INFO germline.py --out = [outDir]
[2023-09-08 15:29:32,726] INFO germline.py --app_path = [apps]
[2023-09-08 15:29:32,726] INFO germline.py --max_mismatch = [3]
[2023-09-08 15:29:32,726] INFO germline.py --nthreads = [1]
Traceback (most recent call last):
File "/Users/moo4005/Desktop/monopo/Monopogen/src/Monopogen.py", line 435, in
The docs say
-b BAMFILE, --bamFile BAMFILE
The bam file for the study sample, the bam file should be sorted. If there are multiple samples, each row with each sample (default: None)
which seems to say you should provide the path to the BAM file but this is wrong. You're getting the unicode error because the code is trying to read a text file, but BAM is binary.
Instead, you should provide the path to a text file that lists the samples and their BAM files. For the example, this file worked for me (save as example/bam.lst
):
A,example/A.bam
B,example/B.bam
And then run python src/Monopogen.py preProcess -b example/bam.lst -o out -a apps
@slinnarsson thank you so much for your help.
I have created a bam.lst file in the example folder and put in it
A,example/A.bam
B,example/B.bam
I ran this python src/Monopogen.py preProcess -b example/A.bam -o out -a apps
but I still get the same error. could you please explain a little bit more how to solve it?
Thanks
Sorry you should provide the list file not the Bam: ”-b example/bam.lst”
@slinnarsson thanks a lot! would you please instruct me how to write the names of the bams in the .lst file.
Hello, thank you so much for developing Monopogen.
I get this error when I run the preProcess module. I tried my bam files and also the bam files you provided as example and unfortunately the issue do exist. I also tried it on python 3.8 and python 3.11 however, the issue is not resolved.
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
I would be very grateful if you could help me with that Thanks