names.filelist

[SashaNikolaevaBerkeley]

I've been trying to calculate genotype likelihoods on a test file (30gb), but I keep getting this error:

python3 Genotype_Likelihoods.py output.file.mpileup
Seed is not set.
Default ploidy levels to be tested in analysis are: [1, 2, 3, 4, 5, 6]
utg000001l 235 T 2 ^).^&. EE )& file is not supported. Supported file types are '.mpileup', '.mpileup.gz' and '.bam'.

I've tried with both .mpileup file and with .bam file. For the .bam the traceback is as follows:

Seed is not set.
Default ploidy levels to be tested in analysis are: [1, 2, 3, 4, 5, 6]
Traceback (most recent call last):
File "/Users/sashanikolaeva/Desktop/HMMploidy-master/Genotype_Likelihoods.py", line 73, in
line = line.decode().strip('\n') # convert bytes into strings
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

I assume it must be an issue with my file, but I have no idea what it might be. My other guess was that maybe it is because I am giving it an individual file and not names.filelist?

Any suggestions?

Thank you!

[SamueleSoraggi]

Hi, I think the problem is that you should give a file list containing which files you want to analyze (in your case only one file). So for example a file called names.filelist which contains only one line of text, which is your file output.file.mpileup. Samuele Den man. 19. sep. 2022 kl. 22.06 skrev SashaNikolaevaBerkeley < ***@***.***>:

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I've been trying to calculate genotype likelihoods on a test file (30gb), but I keep getting this error: python3 Genotype_Likelihoods.py output.file.mpileup Seed is not set. Default ploidy levels to be tested in analysis are: [1, 2, 3, 4, 5, 6] utg000001l 235 T 2 ^).^&. EE )& file is not supported. Supported file types are '.mpileup', '.mpileup.gz' and '.bam'. I've tried with both .mpileup file and with .bam file. For the .bam the traceback is as follows: Seed is not set. Default ploidy levels to be tested in analysis are: [1, 2, 3, 4, 5, 6] Traceback (most recent call last): File "/Users/sashanikolaeva/Desktop/HMMploidy-master/Genotype_Likelihoods.py", line 73, in line = line.decode().strip('\n') # convert bytes into strings UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte I assume it must be an issue with my file, but I have no idea what it might be. My other guess was that maybe it is because I am giving it an individual file and not names.filelist? Any suggestions? Thank you! — Reply to this email directly, view it on GitHub <#8>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACC66UPHPBCWTIY4S2PJDSDV7DBUHANCNFSM6AAAAAAQQNRDDA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[SashaNikolaevaBerkeley]

That didn't help, unfortunately. I created a text file with just one line, which is my output.file.mpileup file, but it still says that the format is not supported. I am on Mac M1, for reference. I've had some issues running code on my computer, but file formats were usually fine.

Ok, I figured that the mpileup file had to be in the same folder as the HMMploidy script in order for it to run properly. It didn't like that I put the entire address of the file into names.filelist (I had the file in a separate folder and provided the address in the names.filelist).