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B-UMMI / chewBBACA

BSR-Based Allele Calling Algorithm
GNU General Public License v3.0
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AttributeError: 'NoneType' object has no attribute 'seq' #164

Closed famiji closed 1 year ago

famiji commented 1 year ago 
 Package                         Version  Build                Channel                                                                Size
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(chewie2) fmj@qood:~$ chewBBACA.py AlleleCall -i /mnt/c/users/26537/desktop/papercpmlst -g /mnt/c/users/26537/desktop/cpmlst/cpcgmlst -o /mnt/c/users/26537/desktop/cpmlst/result --ptf /mnt/c/users/26537/desktop/cpmlst/ATCC13124.trn --cpu 2 --force

chewBBACA version: 3.1.0
Authors: Mickael Silva, Pedro Cerqueira, Rafael Mamede
Github: https://github.com/B-UMMI/chewBBACA
Documentation: https://chewbbaca.readthedocs.io/en/latest/index.html
Contacts: imm-bioinfo@medicina.ulisboa.pt

==========================
  chewBBACA - AlleleCall
==========================
Started at: 2023-03-10T20:54:27

Output directory exists. Will store results in /mnt/c/users/26537/desktop/cpmlst/result/results_20230310T205427.
Minimum sequence length: 0
Size threshold: 0.2
Translation table: 11
BLAST Score Ratio: 0.6
Word size: 5
Window size: 5
Clustering similarity: 0.2
Prodigal training file: /mnt/c/users/26537/desktop/cpmlst/ATCC13124.trn
CPU cores: 2
BLAST path: /home/fmj/miniconda3/envs/chewie2/bin
CDS input: False
Prodigal mode: single
Mode: 4
Number of inputs: 158
Number of loci: 1431

== CDS prediction ==

Predicting CDS for 158 inputs...
 [====================] 100%

== CDS extraction ==

Extracting predicted CDS for 158 inputs...
 [====================] 100%
Extracted a total of 480070 CDS from 158 inputs.

== CDS deduplication ==

Identifying distinct CDS...identified 176116 distinct CDS.

== CDS exact matches ==

Searching for DNA exact matches...found 198392 exact matches (matching 53264 distinct alleles).
Unclassified CDS: 122852

== CDS translation ==

Translating 122852 CDS...
 [====================] 100%
Identified 581 CDS that could not be translated.
Information about untranslatable and small sequences stored in /mnt/c/users/26537/desktop/cpmlst/result/results_20230310T205427/temp/invalid_cds.txt
Unclassified CDS: 122271

== Protein deduplication ==

Identifying distinct proteins...identified 97191 distinct proteins.

== Protein exact matches ==

Searching for Protein exact matches...found 3915 exact matches (6068 distinct CDS, 7203 total CDS).
Unclassified proteins: 93276

== Clustering ==

Translating schema's representative alleles...done.
Creating minimizer index for representative alleles...done.
Created index with 120575 distinct minimizers for 1431 loci.
Clustering proteins...
 [====================] 100%
Clustered 93276 proteins into 1376 clusters.
Clusters to BLAST: 1376
 [====================] 100%
Classifying clustered proteins...
 [====================] 100%
Classified 8674 distinct proteins.
Unclassified proteins: 84602

== Representative determination ==

Iteration 1
===========
Loci: 1431
BLASTing loci representatives against unclassified proteins...done.
Traceback (most recent call last):
  File "/home/fmj/miniconda3/envs/chewie2/bin/chewBBACA.py", line 10, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/chewBBACA.py", line 1584, in main
    functions_info[process][1]()
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/utils/process_datetime.py", line 146, in wrapper
    func(*args, **kwargs)
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/chewBBACA.py", line 514, in allele_call
    AlleleCall.main(genome_list, loci_list, args.schema_directory,
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/AlleleCall/AlleleCall.py", line 2671, in main
    results = allele_calling(input_files, schema_directory, temp_directory,
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/AlleleCall/AlleleCall.py", line 2464, in allele_calling
    locus_results = expand_matches(match_info, prot_index, dna_index,
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/fmj/miniconda3/envs/chewie2/lib/python3.11/site-packages/CHEWBBACA/AlleleCall/AlleleCall.py", line 1388, in expand_matches
    target_protein = str(pfasta_index.get(target_id).seq)
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'seq'
famiji commented 1 year ago

when i try to AlleleCall , there is a error.the information is listed above.

rfm-targa commented 1 year ago

Hello @famiji,

The error you're getting indicates that there is a sequence missing from a FASTA file. It's trying to get the sequence based on the sequence identifier. Strangely, it cannot retrieve a sequence already read in previous steps of the process. Please retry after downgrading BLAST to v2.9 and updating chewBBACA to v3.1.2. If the error persists after that, I suggest you recreate the schema and retry the allele calling. If that doesn't solve the issue, could you send us the schema and the input files to test and find the cause?

Best regards,

Rafael

famiji commented 1 year ago

I downgrade BLAST to v2.9 and successed. Thakns for your patient reply.

Nilad commented 1 year ago

Have same error with chewBBACA version: 3.1.2 and blast 2.12.0, build Mar 8 2022 16:19:08.

Error solved with downgrade of BLAST to v2.9.0

rfm-targa commented 1 year ago

Hello @Nilad,

Thank you for reporting that. We'll try to look into why BLAST 2.12 is leading to this issue and include a fix in one of the next releases.

Kind regards,

Rafael