I am getting this error whiile creating manifest file, importing and other downstream application. Can anyone help on this?

Namraj_Jaishi · June 13, 2024, 12:42pm

It appears like this but I get the output.

UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)

cherman2 · June 13, 2024, 4:49pm

Hi @Namraj_Jaishi.
We need alot more information in order to help you!

what QIIME 2 env are you using?
what commands are you running?
How are you creating the manifest file?

Namraj_Jaishi · June 13, 2024, 6:56pm

I am using "qiime2-amplicon-2024.5-py38-linux-conda.yml".
I created manifest file by :
sample-id,absolute-filepath,direction

5,/mnt/c/Users/Namraj Jaishi/Desktop/16S/5/5R1.gz,forward

5,/mnt/c/Users/Namraj Jaishi/Desktop/16S/5/5R2.gz,reverse

6,/mnt/c/Users/Namraj Jaishi/Desktop/16S/6/6R1.gz,forward

6,/mnt/c/Users/Namraj Jaishi/Desktop/16S/6/6R2.gz,reverse

Every code gets executed but at the same time, it shows the error as well. I updated conda as a whole and numpy separately "conda update conda"
using "conda update lumpy" respectively.
During the steps of importing, quality control, and denoising with DADA2, I also got that error with the execution of code.

cherman2 · June 13, 2024, 10:17pm

@Namraj_Jaishi,
I am not exactly sure what this issue is!

I found this error online but I am not sure if it is helpful. UserWarning of `numpy.longdouble` trigger when importing h5py with numpy>=1.25 · Issue #2357 · h5py/h5py · GitHub

Have you tried uninstalling qiime2 and reinstalling it?

Let me know!

Namraj_Jaishi · June 16, 2024, 2:22pm

It stills shows the same after uninstalling and re installing.
I am getting this error while importing:
There was a problem importing 16Smanifestfile.tsv:

16Smanifestfile.tsv is not a(n) PairedEndFastqManifestPhred33V2 file:

I have used this code:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path 16Smanifestfile.tsv
--output-path paired-end-demux.qza
--input-format PairedEndFastqManifestPhred33V2
It is not letting me to import. Please help

colinvwood · June 17, 2024, 5:02pm

Hello @Namraj_Jaishi,

I believe the PairedEndFastqManifestPhred33V2 format expects a forward-absolute-filepath column and a reverse-absolute-filepath column. You can see an example here.

Namraj_Jaishi · June 18, 2024, 6:54pm

I am getting this error again and again. I tried installing Qiime 2 amplicon 2024.5 on the school computer but encountered the same issue.
Both devices are Windows . My terminal is Ubuntu, WSL.

My code is:
qiime diversity core-metrics-phylogenetic
--i-phylogeny rooted-tree.qza
--i-table table.qza
--p-sampling-depth 6
--m-metadata-file metadata.tsv
--output-dir core-metrics-results

The error is:
/home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)
Plugin error from diversity:

Command '['faithpd', '-i', '/tmp/qiime2/jaishi452/data/51777971-b269-437f-be98-0fd4669e7de6/data/feature-table.biom', '-t', '/tmp/qiime2/jaishi452/data/22e7cd11-48b0-4c28-9cff-e43a246a0d8f/data/tree.nwk', '-o', '/tmp/q2-AlphaDiversityFormat-fs2xwhie']' returned non-zero exit status 126.

Debug info has been saved to /tmp/qiime2-q2cli-err-uw4tr02z.log
I have uninstalled, installed, and updated everything.
Can somebody help with this ?

This issue " /home/jaishi452/miniconda3/envs/qiime2-amplicon-2024.5/lib/python3.9/site-packages/numpy/core/getlimits.py:542: UserWarning: Signature b'\x00\xd0\xcc\xcc\xcc\xcc\xcc\xcc\xfb\xbf\x00\x00\x00\x00\x00\x00' for <class 'numpy.longdouble'> does not match any known type: falling back to type probe function.
This warnings indicates broken support for the dtype!
machar = _get_machar(dtype)" appears everytime when I execute for importing, denoising , feature table generation but the code gets executed . While during alpha and beta diversity analysis, code doesn't get executed.

jwdebelius · June 18, 2024, 7:42pm

Hi @Namraj_Jaishi,

I've combined your topics, because it seems like you're having the same issue, but one is productive and the other is breaking.

One thought is your region. This is an encoding issue. Maybe look at how to change your locale ot a UTF-8 locale on WSL and see if that helps.

A second question is why things are breaking where. Core Diveristy Metrics involves several steps. So, if import, denoising, and the feature table work, but the core diveristy doesn't, it might be good to isolate where the core diversity is failing. One difference might be the construction of a visualization. Have you tried visualizing your feature table through q2-feature-table summarize and checking your denoising stats?

If that works, please try adding your metadata to your feature table summary, becuase that might be another place to have an encoding issue that would be parallel to a beta diversity step that might be failing.

Best,
Justine

Mike_Stevenson · July 16, 2024, 6:24am

Hi @Namraj_Jaishi did you get sorted with this problem? When I was trying to sort out an import/manifest problem, the ‘PairedEndFastqManifestPhred33V2‘ was causing compatibility issues for me. I removed the ‘V2’ from the end and it worked for me. Just thought it might be worth trying.

Also, I noticed in your first comment your manifest file format was comma-delimited, but further down the post, this had changed. If it is in CSV format, I found that I needed to save it in something like TextEdit app first and then rename with the .csv extension.

Best of luck!

system · August 16, 2024, 12:24pm

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