b-ummi / innuca Goto Github PK

Dear INNUCA team,

Is it possible to run INNUCA for other species than the one listed in the below modules?

https://github.com/B-UMMI/INNUca/tree/master/modules/trueCoverage_rematch
campylobacter_jejuni.config
v2.3
5 years ago
campylobacter_jejuni.fasta
v2.3
5 years ago
combine_trueCoverage_reports.py
v3.1
5 years ago
escherichia_coli.config
v3.1
5 years ago
escherichia_coli.fasta
v2.5
5 years ago
haemophilus_influenzae.config
Make trueCoverage executable and add references for other species
4 years ago
haemophilus_influenzae.fasta
Make trueCoverage executable and add references for other species
4 years ago
listeria_monocytogenes.config
Change Listeria monocytogenes trueCoverage defaults and sequences
4 years ago
listeria_monocytogenes.fasta
Properly format fasta
4 years ago
salmonella_enterica.config
v2.5
5 years ago
salmonella_enterica.fasta
v2.5
5 years ago
streptococcus_agalactiae.config
v2.3
5 years ago
streptococcus_agalactiae.fasta
v2.5
5 years ago
streptococcus_dysgalactiae.config
Make trueCoverage executable and add references for other species
4 years ago
streptococcus_dysgalactiae.fasta
Make trueCoverage executable and add references for other species
4 years ago
streptococcus_pneumoniae.config
Make trueCoverage executable and add references for other species
4 years ago
streptococcus_pneumoniae.fasta
Make trueCoverage executable and add references for other species
4 years ago
streptococcus_pyogenes.config
Make trueCoverage executable and add references for other species
4 years ago
streptococcus_pyogenes.fasta
Make trueCoverage executable and add references for other species
4 years ago
yersinia_enterocolitica.config
v2.3
5 years ago
yersinia_enterocolitica.fasta
v2.3
5 years ago

Kindly clarify what are the additional things needed to setup for analysis of pseudomonas aeruginosa, Enterobacter cloacae and ralstonia mannitolilytica species?

Best Regards,
Bala

We are planing to use trueCoverage_rematch.py in one of our pipelines.

1. is it possible to use only that module? or do we need to install the whole INNUca?
2. And, is there any documentation on that module on the steps involved in the module to understand how it works?

Thanks

Dear INNUCA team,

Is there any documentation somewhere about the below field values mentioned in the combined_report.py scripy?

fields = ['#samples',
'number_reads_sequenced', 'number_bp_sequenced',
'min_reads_length', 'max_reads_length',
'reads_kraken_number_taxon_found', 'reads_kraken_percentage_unknown_fragments',
'reads_kraken_most_abundant_taxon', 'reads_kraken_percentage_most_abundant_taxon',
'first_coverage',
'trueCoverage_absent_genes', 'trueCoverage_multiple_alleles', 'trueCoverage_sample_coverage',
'second_Coverage',
'pear_assembled_reads', 'pear_unassembled_reads', 'pear_dicarded_reads',
'SPAdes_number_contigs', 'SPAdes_number_bp', 'SPAdes_filtered_contigs', 'SPAdes_filtered_bp',
'assembly_coverage_initial', 'assembly_coverage_filtered', 'mapped_reads_percentage',
'mapping_filtered_contigs', 'mapping_filtered_bp',
'Pilon_changes', 'Pilon_contigs_changed', 'Pilon_contigs', 'Pilon_bp',
'MLST_scheme', 'MLST_ST',
'assembly_kraken_number_taxon_found', 'assembly_kraken_percentage_unknown_fragments',
'assembly_kraken_most_abundant_taxon', 'assembly_kraken_percentage_most_abundant_taxon',
'insert_size_mean', 'insert_size_sd',
'final_assembly']

I would like to know some minimum information about these field values. Although most of the values were straight-forward, i like to know for sure that it means the same thing if you have some documentation for these values.

Thanks in advance,

Best Regards,
Bala

Dear Innuca Team,

I notice that INNUCA uses tuberfree-mlst biocontainers (ummidock-mlst-tuberfree.img) for the Yersinia enterocolitica analysis. When i look into carefully, i notice the removal of ypseudotuberculosis_achtman_3 folder is done within the database inside the containers in order to make default usage of McNally scheme over achtman scheme. May i know what is the rationale of selection of McNally scheme over achtman scheme?

Best Regards,
Bala

As python2 will die at the end of this year, INNUca should me moved to use python3.

Hi,

Apparently I cannot use docker in my desktop so I followed the stand alone steps to install INNUca, and I got the following error when running the test script:

RUNNING FastQ integrity check

Fastq quality encoding: Sanger
Runtime :0.0h:0.0m:20.26s
END FastQ integrity check

RUNNING Estimated Coverage analysis

Estimated depth coverage: 93.4x
Runtime :0.0h:0.0m:6.52s
END Estimated Coverage analysis

RUNNING True coverage check

Traceback (most recent call last):
  File "/home/shlomo/Programs/INNUca/test_INNUca/../INNUca.py", line 847, in <module>
    main()
  File "/home/shlomo/Programs/INNUca/test_INNUca/../INNUca.py", line 277, in main
    species_genus, mlst_scheme_genus, spades_version=spades_version)
  File "/home/shlomo/Programs/INNUca/test_INNUca/../INNUca.py", line 493, in run_innuca
    clean_run_rematch=True)
  File "/home/shlomo/Programs/INNUca/modules/utils.py", line 876, in wrapper
    results = list(function(*args, **kwargs))  # guarantees return is a list to allow .insert()
  File "/home/shlomo/Programs/INNUca/modules/trueCoverage_rematch.py", line 181, in run_true_coverage
    import rematch_module
ImportError: No module named rematch_module

Problem running INNUca

Appreciate some help with this... (ReMatch is in the $PATH).

Hi, Are you guys planning to add this to the galaxy tool shed? so its east to use