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rfm-targa committed Feb 23, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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# Changelog

## 3.3.3 - 2024-02-21
## 3.3.3 - 2024-02-23

- Fixed warning related with BLASTp `--seqidlist` parameter. For BLAST>=2.9, the TXT file with the sequence IDs is converted to binary format with `blastdb_aliastool`.

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213 changes: 108 additions & 105 deletions CHEWBBACA/docs/user/tutorials/chewieNS_step_by_step.rst
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Expand Up @@ -240,7 +240,7 @@ To download the schema you have uploaded, please run the following command:

Downloading compressed version...
Decompressing schema...
Schema is now available at: sagalactiae_ns/sagalactiae_tut
Schema is now available at: sagalactiae_ns/Streptococcus_agalactiae_tut

The process will download a ready-to-use schema to the output directory you have specified.
The loci and alleles included in the schema are the same that were in the original schema,
Expand Down Expand Up @@ -274,12 +274,14 @@ the following command:

::

$ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset1/ -g sagalactiae_ns/sagalactiae_tut/ -o subset1_results
$ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset1/ -g sagalactiae_ns/Streptococcus_agalactiae_tut/ -o subset1_results

==========================
chewBBACA - AlleleCall
==========================

Configuration values
======================
Minimum sequence length: 201
Size threshold: 0.2
Translation table: 11
Expand All @@ -289,111 +291,117 @@ the following command:
Clustering similarity: 0.2
Prodigal training file: Streptococcus_agalactiae.trn
CPU cores: 1
BLAST path: /home/user/.conda/envs/env/bin
BLAST path: /home/user/envs/chewie333/bin
CDS input: False
Prodigal mode: single
Mode: 4
Number of inputs: 12
Number of loci: 10

Determining sequence length mode for all loci...done.

Creating pre-computed hash tables...done.

== CDS prediction ==

Predicting CDS for 12 inputs...
Intermediate files will be stored in subset1_results/temp

Pre-computed data
===================
Determining allele size mode for all loci...
Loci allele size mode values stored in sagalactiae_ns/Streptococcus_agalactiae_tut/loci_modes
Could not find pre-computed hash tables used for exact matching.
Creating hash tables...
Hash tables stored in sagalactiae_ns/Streptococcus_agalactiae_tut/pre_computed

CDS prediction
================
Predicting CDSs for 12 inputs...
[====================] 100%

== CDS extraction ==

Extracting predicted CDS for 12 inputs...
Extracted a total of 24282 CDSs from 12 inputs.

CDS deduplication
===================
Identifying distinct CDSs...
Identified 14751 distinct CDSs.

CDS exact matching
====================
Searching for CDS exact matches...
Found 2 exact matches (2 distinct schema alleles).
Unclassified CDSs: 14749

CDS translation
=================
Translating 14749 CDSs...
[====================] 100%
Extracted a total of 24282 CDS from 12 inputs.

== CDS deduplication ==

Identifying distinct CDS...identified 14751 distinct CDS.

== CDS exact matches ==

Searching for DNA exact matches...found 2 exact matches (matching 2 distinct alleles).
Unclassified CDS: 14749

== CDS translation ==

Translating 14749 CDS...
[====================] 100%
Identified 428 CDS that could not be translated.
Information about untranslatable and small sequences stored in subset1_results/temp/invalid_cds.txt
Unclassified CDS: 14321

== Protein deduplication ==

Identifying distinct proteins...identified 11319 distinct proteins.

== Protein exact matches ==

Searching for Protein exact matches...found 1 exact matches (2 distinct CDS, 2 total CDS).
428 CDSs could not be translated.
Unclassified CDSs: 14321

Protein deduplication
=======================
Identifying distinct proteins...
Identified 11319 distinct proteins.

Protein exact matching
========================
Searching for Protein exact matches...
Found 1 exact matches (2 distinct CDSs, 2 total CDSs).
Unclassified proteins: 11318

== Clustering ==

Translating schema's representative alleles...done.
Determining BLASTp raw score for each representative...done.
Creating minimizer index for representative alleles...done.
Protein clustering
====================
Translating schema representative alleles...
Determining BLASTp self-score for each representative...
Representative BLASTp self-scores stored in sagalactiae_ns/Streptococcus_agalactiae_tut/short/self_scores
Creating minimizer index for representative alleles...
Created index with 2400 distinct minimizers for 10 loci.
Clustering proteins...
[====================] 100%
Clustered 11318 proteins into 7 clusters.
Clusters to BLAST: 7
Clustered 58 proteins into 7 clusters.
11260 proteins were not added to any cluster.
Aligning cluster representatives against clustered proteins...
[====================] 100%
Classifying clustered proteins...
Classifying high-scoring matches...
[====================] 100%
Classified 40 distinct proteins.
Unclassified proteins: 11278

== Representative determination ==

Iteration 1
===========
Loci: 10
BLASTing loci representatives against unclassified proteins...done.
Loci with high-scoring matches: 1
Classifying proteins...classified 3 proteins.
Selecting representatives for next iteration...selected 1 representatives.
Unclassified proteins: 11275

Iteration 2
===========
Loci: 1
BLASTing loci representatives against unclassified proteins...done.
Loci with high-scoring matches: 1
Classifying proteins...classified 1 proteins.
Unclassified proteins: 11274

== Wrapping up ==

Writing results_contigsInfo.tsv...done.
Writing paralogous_loci.tsv and paralogous_counts.tsv...done.
Detected number of paralogous loci: 0
Writing logging_info.txt...done.
Writing results_alleles.tsv...done.
Writing results_statistics.tsv...done.
Writing loci_summary_stats.tsv...done.
Representative determination
==============================
Aligning representative alleles against unclassified proteins...
===========================================================================
Iteration Loci High-Scoring Classified Selected Unclassified
===========================================================================
1 10 1 3 1 11275
2 1 1 1 0 11274
===========================================================================

Wrapping up
=============
Creating file with genome coordinates profiles (results_contigsInfo.tsv)...
Identifying paralogous loci and creating files with the list of paralogous loci (paralogous_counts.tsv & paralogous_loci.tsv)...
Identified 0 paralogous loci.
Assigning allele identifiers to inferred alleles...
Assigned identifiers to 47 new alleles for 7 loci.
Getting original sequence identifiers for new alleles...
Getting data for new representative alleles...
Adding the BLASTp self-score for the new representatives to sagalactiae_ns/Streptococcus_agalactiae_tut/short/self_scores
Creating FASTA files with the new alleles...
Adding new alleles to schema...
Updating allele size mode values stored in sagalactiae_ns/Streptococcus_agalactiae_tut/loci_modes
Updating pre-computed hash tables in sagalactiae_ns/Streptococcus_agalactiae_tut/pre_computed
Creating file with the allelic profiles (results_alleles.tsv)...
Creating file with class counts per input (results_statistics.tsv)...
Creating file with class counts per locus (loci_summary_stats.tsv)...
Creating file with the coordinates of CDSs identified in inputs (cds_coordinates.tsv)...
Creating file with invalid CDSs (invalid_cds.txt)...
Counting number of classified CDSs...
Classified a total of 67 CDSs.
INF: 47
EXC: 17
ASM: 3
PLOT3: 0
PLOT5: 0
LOTSC: 0
NIPH: 0
NIPHEM: 0
ALM: 0
PAMA: 0
Added 47 novel alleles to schema.
Added 1 representative alleles to schema.
=========================================================================================
EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA
=========================================================================================
17 47 0 0 0 0 0 0 3 0
=========================================================================================
Added 47 new alleles to the schema.
Added 1 new representative alleles to the schema.
Removing temporary directory with intermediate files...
Creating log file (logging_info.txt)...

Results available in subset1_results

The ``AlleleCall`` process will print the total number of classified CDSs per classification category to the standard
output. You can see a :doc:`detailed description </user/modules/AlleleCall>`
Expand Down Expand Up @@ -449,7 +457,7 @@ downloaded from).

::

$ chewBBACA.py SyncSchema -sc sagalactiae_ns/sagalactiae_tut/ --submit
$ chewBBACA.py SyncSchema -sc sagalactiae_ns/Streptococcus_agalactiae_tut/ --submit

==========================
chewBBACA - SyncSchema
Expand Down Expand Up @@ -570,7 +578,7 @@ A sample command would be:
Number of invalid alleles: 0

Successfully adapted 10/10 loci present in the input schema.
Schema is now available at: sagalactiae_snapshot/sagalactiae_tut
Schema is now available at: sagalactiae_snapshot/Streptococcus_agalactiae_tut

This will download all FASTA files for all loci in the schema and construct the schema locally.
Since we have requested for the schema in a state prior to its ``Last Change Date``, we will
Expand All @@ -587,23 +595,18 @@ match.

::

$ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset2/ -g sagalactiae_snapshot/sagalactiae_tut/ -o subset2_results
$ chewBBACA.py AlleleCall -i sagalactiae_genomes/subset2/ -g sagalactiae_snapshot/Streptococcus_agalactiae_tut/ -o subset2_results

...

Classified a total of 75 CDSs.
INF: 49
EXC: 25
ASM: 1
PLOT3: 0
PLOT5: 0
LOTSC: 0
NIPH: 0
NIPHEM: 0
ALM: 0
PAMA: 0
Added 49 novel alleles to schema.
Added 1 representative alleles to schema.
=========================================================================================
EXC INF PLOT3 PLOT5 LOTSC NIPH NIPHEM ALM ASM PAMA
=========================================================================================
25 49 0 0 0 0 0 0 1 0
=========================================================================================
Added 49 new alleles to the schema.
Added 1 new representative alleles to the schema.

...

Expand Down Expand Up @@ -631,7 +634,7 @@ To perform this last synchronization, execute:

::

$ chewBBACA.py SyncSchema -sc sagalactiae_snapshot/sagalactiae_tut/ --submit
$ chewBBACA.py SyncSchema -sc sagalactiae_snapshot/Streptococcus_agalactiae_tut/ --submit

...

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2 changes: 1 addition & 1 deletion CHEWBBACA/docs/user/tutorials/chewie_step_by_step.rst
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Expand Up @@ -24,7 +24,7 @@ Please start by going through the following steps:
The expected results for each section were included in the ``expected_results`` folder
for reference (each subfolder has the name of one of the sections).

Metadata about the NCBI genomes used in this tutorial is available on the TSV file ``genomes/GBS_NCBI_metadata.tsv``.
Metadata about the NCBI genomes used in this tutorial is available on the TSV file ``genomes/sagalactiae_NCBI_metadata.tsv``.

chewBBACA includes Prodigal training files for several species, including for
*Streptococcus agalactiae*. You can check the list of available training files
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -21,7 +21,7 @@ settings and a set of functions to visualize and validate allele variation in th

## News

## 3.3.3 - 2024-02-21
## 3.3.3 - 2024-02-23

- Fixed warning related with BLASTp `--seqidlist` parameter. For BLAST>=2.9, the TXT file with the sequence IDs is converted to binary format with `blastdb_aliastool`.

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