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snayfach / MicrobeCensus

MicrobeCensus estimates the average genome size of microbial communities from metagenomic data
http://genomebiology.com/2015/16/1/51
GNU General Public License v3.0
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TypeError: cannot unpack non-iterable NoneType object in run_microbe_census.py #32

Open shanexuuu opened 5 months ago

shanexuuu commented 5 months ago

Hi,

Met a typeerror issue in conda microbecensus v1.1.1. Could you give my any suggestion? Many thanks!

My running code: run_microbe_census.py -t 100 -n 100000000 SK0108G_A_1.fastq,SK0108G_A_2.fastq microbecensus/SK0108G_A_out

Error: a bytes-like object is required, not 'str' Traceback (most recent call last): File "run_microbe_census.py", line 62, in est_ags, args = microbe_census.run_pipeline(args) ^^^^^^^^^^^^^ TypeError: cannot unpack non-iterable NoneType object

kangluyao commented 4 months ago

Hi, @shanexuuu, I also encounter the same issue in conda microbecensus, have you resolved it?

shanexuuu commented 4 months ago

Hi,

Nope. I fount RPKG and RPKM result are highly similar. So I switched to RPKM and also TPM.

发件人: Luyao Kang @.> 发送时间: 2024年3月8日 15:51 收件人: snayfach/MicrobeCensus @.> 抄送: XU Wenqian @.>; Mention @.> 主题: Re: [snayfach/MicrobeCensus] TypeError: cannot unpack non-iterable NoneType object in run_microbe_census.py (Issue #32)

Hi, @shanexuuuhttps://github.com/shanexuuu, I also encounter the same issue in conda microbecensus, have you resolved it?

― Reply to this email directly, view it on GitHubhttps://github.com/snayfach/MicrobeCensus/issues/32#issuecomment-1985210026, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A3ETTBXKENBSAUCBGPSMZVLYXFUXVAVCNFSM6AAAAABCWCZ5Q6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSOBVGIYTAMBSGY. You are receiving this because you were mentioned.Message ID: @.***>

shanexuuu commented 3 months ago

I see. Thank you very much!

Best, Wenqian

From: Jocker @.> Sent: Friday, March 29, 2024 10:04:33 AM To: snayfach/MicrobeCensus @.> Cc: XU Wenqian @.>; Mention @.> Subject: Re: [snayfach/MicrobeCensus] TypeError: cannot unpack non-iterable NoneType object in run_microbe_census.py (Issue #32)

Hello, I met the same problem. When python3 is default version, .gz file will be treated as tar.gz. Changing open_file function in commicrobe_census.py in microbe_censes package path could work. image.png (view on web)https://github.com/snayfach/MicrobeCensus/assets/35793183/7b23c2e1-dad7-4f97-8466-b1f790054186

— Reply to this email directly, view it on GitHubhttps://github.com/snayfach/MicrobeCensus/issues/32#issuecomment-2026472218, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A3ETTBTANGQVXLO6FGLUT73Y2TD3DAVCNFSM6AAAAABCWCZ5Q6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMRWGQ3TEMRRHA. You are receiving this because you were mentioned.Message ID: @.***>

KatherineDuchesneau commented 2 months ago

Hi, I found a solution to this error. Its a python version issue. If you installed via a conda environment, get it from bioconda, or make sure python is version 2.7