[2024-01-24 15:02:36,437] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference
[2024-01-24 15:02:38,277] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,279] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6794937-ebe4-4156-a28f-0a78b885d0fb/GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/cds.fna -a GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:45,580] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:45,580] [INFO] Task started: HMMsearch
[2024-01-24 15:02:45,580] [INFO] Running command: hmmsearch --tblout GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/reference_markers.hmm GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:45,919] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:45,921] [INFO] Found 6/6 markers.
[2024-01-24 15:02:45,944] [INFO] Query marker FASTA was written to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:02:45,944] [INFO] Task started: Blastn
[2024-01-24 15:02:45,944] [INFO] Running command: blastn -query GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/reference_markers.fasta -out GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:48,018] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:48,021] [INFO] Selected 15 target genomes.
[2024-01-24 15:02:48,022] [INFO] Target genome list was writen to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:02:48,038] [INFO] Task started: fastANI
[2024-01-24 15:02:48,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6794937-ebe4-4156-a28f-0a78b885d0fb/GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna.gz --refList GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:56,599] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:56,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:56,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:56,611] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:02:56,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:56,611] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	100.0	737	743	95	conclusive
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	99.9839	723	743	95	conclusive
Moraxella cuniculi	strain=NCTC10297	GCA_900637105.1	34061	34061	type	True	98.214	635	743	95	conclusive
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	79.3943	280	743	95	below_threshold
Moraxella pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	79.0626	291	743	95	below_threshold
Moraxella nasovis	strain=ZY201115	GCA_022701215.1	2904121	2904121	type	True	78.1575	151	743	95	below_threshold
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	77.9854	239	743	95	below_threshold
Moraxella equi	strain=NCTC11012	GCA_900453335.1	60442	60442	type	True	77.7499	173	743	95	below_threshold
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	77.6967	174	743	95	below_threshold
Moraxella oblonga	strain=NBRC 102422	GCA_001598275.1	200413	200413	type	True	77.439	152	743	95	below_threshold
Psychrobacter celer	strain=DSM 23510	GCA_016107555.1	306572	306572	type	True	76.7314	56	743	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:56,613] [INFO] DFAST Taxonomy check result was written to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:02:56,614] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:56,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:56,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/checkm_data
[2024-01-24 15:02:56,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:56,644] [INFO] Task started: CheckM
[2024-01-24 15:02:56,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/checkm_input GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:03:25,526] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:25,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:25,557] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:25,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:25,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:03:25,558] [INFO] Task started: Blastn
[2024-01-24 15:03:25,559] [INFO] Running command: blastn -query GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg10ad7cc3-ab19-45e3-a6ec-d12ccfde7602/dqc_reference/reference_markers_gtdb.fasta -out GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:26,720] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:26,723] [INFO] Selected 15 target genomes.
[2024-01-24 15:03:26,723] [INFO] Target genome list was writen to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:26,757] [INFO] Task started: fastANI
[2024-01-24 15:03:26,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6794937-ebe4-4156-a28f-0a78b885d0fb/GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna.gz --refList GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:34,432] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:34,443] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:34,444] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900156515.1	s__Moraxella cuniculi	100.0	737	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	conclusive
GCF_002014855.1	s__Moraxella porci	79.4123	279	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_002014825.1	s__Moraxella pluranimalium	79.0862	289	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002014965.1	s__Moraxella canis	78.4813	262	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_001656295.1	s__Moraxella catarrhalis_C	78.3282	250	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_001632285.1	s__Moraxella catarrhalis	78.0	238	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_000696305.2	s__Moraxella bovoculi	77.8594	148	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	98.49	98.41	0.96	0.96	5	-
GCF_002027555.1	s__Moraxella equi	77.7016	173	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002014975.1	s__Moraxella bovis	77.4866	167	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_001598275.1	s__Moraxella oblonga	77.4208	153	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107555.1	s__Psychrobacter celer	76.7314	56	743	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Psychrobacter	95.0	97.12	95.68	0.88	0.85	9	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:34,450] [INFO] GTDB search result was written to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:34,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:34,456] [INFO] DFAST_QC result json was written to GCF_900156515.1_IMG-taxon_2681812931_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:03:34,457] [INFO] DFAST_QC completed!
[2024-01-24 15:03:34,457] [INFO] Total running time: 0h0m58s