Picrust2 Analysis _error output

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mashu...@gmail.com

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Apr 12, 2021, 12:16:19 PM4/12/21
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Hi,
1. First I was analyzing Picrusrt2 in qiime2 plugin:
a. Used the following command template

(place_seqs.py -s ../seqs.fna -o out.tre -p 1 \

              --intermediate intermediate/place_seqs)


place_seqs.py -s New_Analysis_with_fna/sequence2.fna -o out46.tre -p 1 \              --intermediate intermediate/place46_seqs

It resulted in  query_align.stockholm file inside place46_seqs (output image attached)

b. followed by this I used this template 

(picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1)

picrust2_pipeline.py -s New_Analysis_with_fna/sequence2.fna -i trial4621/feature-table.biom.tsv -o trial4621 -p 1

 It resusted out error:

(qiime2-2019.10) msiddiq7@enggpz1p23:~/Kang_dataset_picrust$ picrust2_pipeline.py -s New_Analysis_with_fna/sequence2.fna -i trial4621/feature-table.biom.tsv -o trial4621 -p 1

Traceback (most recent call last):

  File "/home/utad/msiddiq7/.conda/envs/qiime2-2019.10/bin/picrust2_pipeline.py", line 264, in <module>

    main()

  File "/home/utad/msiddiq7/.conda/envs/qiime2-2019.10/bin/picrust2_pipeline.py", line 255, in main

    verbose=args.verbose)

  File "/home/utad/msiddiq7/.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/pipeline.py", line 118, in full_pipeline

    check_overlapping_seqs(study_fasta, input_table, verbose)

  File "/home/utad/msiddiq7/.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/pipeline.py", line 361, in check_overlapping_seqs

    FASTA_ASVs = set(read_fasta(in_seq).keys())

  File "/home/utad/msiddiq7/.conda/envs/qiime2-2019.10/lib/python3.6/site-packages/picrust2/util.py", line 63, in read_fasta

    seq[name] += line

KeyError: None

(qiime2-2019.10) msiddiq7@enggpz1p23:~/Kang_dataset_picrust$

I did not understand what it means or how to solve it!

Later on, I have installed picrust2 on another Linux computer and used the following commands :

>>

Template (place_seqs.py -s ../seqs.fna -o out.tre -p 1 \

              --intermediate intermediate/place_seqs)

 

place_seqs.py -s sequence2.fna -o out.tre -p 1 \

              --intermediate intermediate/place_seqs


>> Second command:

Template: (picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1)

 

picrust2_pipeline.py -s sequence2.fna -i feature-table.biom -o picrust2_out_pipeline -p 1

(picrust2) afia@afia-P452LA:~/Desktop/picrust2$ picrust2_pipeline.py -s sequence2.fna -i feature-table.biom -o picrust2_out_pipeline -p 1

Traceback (most recent call last):

  File "/home/afia/miniconda3/envs/picrust2/bin/picrust2_pipeline.py", line 248, in <module>

    main()

  File "/home/afia/miniconda3/envs/picrust2/bin/picrust2_pipeline.py", line 238, in main

    verbose=args.verbose)

  File "/home/afia/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/pipeline.py", line 122, in full_pipeline

    check_overlapping_seqs(study_fasta, input_table, verbose)

  File "/home/afia/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/pipeline.py", line 326, in check_overlapping_seqs

    FASTA_ASVs = set(read_fasta(in_seq).keys())

  File "/home/afia/miniconda3/envs/picrust2/lib/python3.6/site-packages/picrust2/util.py", line 62, in read_fasta

    seq[name] += line

KeyError: None

(picrust2) afia@afia-P452LA:~/Desktop/picrust2$ 


It also resulted in similar output/bugs

Could you please suggest to me what should I do, now?


Thanks in advance 

Mashuk

vi_place_seqs2.jpg

Gavin Douglas

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Apr 12, 2021, 2:41:10 PM4/12/21
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Hey there,

I think the problem is likely that there isn’t an id for each sequence in your input FASTA. Can you confirm whether this is the case or not?

If you post the head of your input FASTA there might be an obvious issue as well.


Thanks,

Gavin

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<vi_place_seqs2.jpg>

Mashuk Siddiquee

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Apr 13, 2021, 10:42:10 AM4/13/21
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Hi Gavin,
Thank you very much for your reply. 
I have checked the sequence2.fna file (created from fasta), could not identify the issue. 
Here is the screenshot of  head sequence2.fna and the specific line that came out in the bug (63,118, 255, 264, 361) from qiime2plugin.
I guess it might help to find a clue.
Thnks
Mashuk




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Regards

Mashuk Siddiquee

E-mail: mashu...@gmail.com  

head_Seq fna.jpg
Seq_point_fna_file.jpg

Gavin Douglas

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Apr 13, 2021, 4:03:03 PM4/13/21
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Hi there,

I’m not sure what the issue is, but if you send me the FASTA file I can take a look and help troubleshoot!


Cheers,

Gavin

To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/CALtY15z%3DiAxL-%3Dg_L%2BwMN9nCfhXuKUYegUzm0WBahYUrdO%3D_9Q%40mail.gmail.com.
<head_Seq fna.jpg><Seq_point_fna_file.jpg>

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