[2024-01-24 12:44:11,507] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference
[2024-01-24 12:44:12,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,840] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,841] [INFO] Running command: gunzip -c /var/lib/cwl/stga29b9ee9-ae3e-405c-9611-63d74150d56d/GCF_016028775.1_ASM1602877v1_genomic.fna.gz | prodigal -d GCF_016028775.1_ASM1602877v1_genomic.fna/cds.fna -a GCF_016028775.1_ASM1602877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:19,502] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:19,502] [INFO] Task started: HMMsearch
[2024-01-24 12:44:19,502] [INFO] Running command: hmmsearch --tblout GCF_016028775.1_ASM1602877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/reference_markers.hmm GCF_016028775.1_ASM1602877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:19,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:19,770] [INFO] Found 6/6 markers.
[2024-01-24 12:44:19,835] [INFO] Query marker FASTA was written to GCF_016028775.1_ASM1602877v1_genomic.fna/markers.fasta
[2024-01-24 12:44:19,836] [INFO] Task started: Blastn
[2024-01-24 12:44:19,836] [INFO] Running command: blastn -query GCF_016028775.1_ASM1602877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/reference_markers.fasta -out GCF_016028775.1_ASM1602877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:20,482] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:20,486] [INFO] Selected 10 target genomes.
[2024-01-24 12:44:20,486] [INFO] Target genome list was writen to GCF_016028775.1_ASM1602877v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:20,492] [INFO] Task started: fastANI
[2024-01-24 12:44:20,492] [INFO] Running command: fastANI --query /var/lib/cwl/stga29b9ee9-ae3e-405c-9611-63d74150d56d/GCF_016028775.1_ASM1602877v1_genomic.fna.gz --refList GCF_016028775.1_ASM1602877v1_genomic.fna/target_genomes.txt --output GCF_016028775.1_ASM1602877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:25,850] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:25,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:25,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:25,864] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:44:25,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:25,864] [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 nonliquefaciens	strain=FDAARGOS_869	GCA_016028775.1	478	478	type	True	100.0	777	780	95	conclusive
Moraxella nonliquefaciens	strain=CCUG 348	GCA_001679005.1	478	478	type	True	99.9605	742	780	95	conclusive
Moraxella lacunata	strain=CCUG 4441	GCA_002027545.1	477	477	suspected-type	True	87.693	566	780	95	below_threshold
Moraxella lacunata	strain=NBRC 102154	GCA_001591245.1	477	477	suspected-type	True	87.6228	513	780	95	below_threshold
Moraxella caprae	strain=NCTC12877	GCA_900453285.1	90240	90240	type	True	84.2841	579	780	95	below_threshold
Moraxella caprae	strain=DSM 19149	GCA_000426885.1	90240	90240	type	True	84.1941	547	780	95	below_threshold
Moraxella equi	strain=CCUG 4950	GCA_002027555.1	60442	60442	type	True	84.1224	513	780	95	below_threshold
Moraxella bovis	strain=CCUG 2133	GCA_002014975.1	476	476	type	True	84.0282	556	780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:25,866] [INFO] DFAST Taxonomy check result was written to GCF_016028775.1_ASM1602877v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:25,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:25,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:25,867] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/checkm_data
[2024-01-24 12:44:25,868] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:25,893] [INFO] Task started: CheckM
[2024-01-24 12:44:25,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028775.1_ASM1602877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028775.1_ASM1602877v1_genomic.fna/checkm_input GCF_016028775.1_ASM1602877v1_genomic.fna/checkm_result
[2024-01-24 12:44:54,009] [INFO] Task succeeded: CheckM
[2024-01-24 12:44:54,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:44:54,032] [INFO] ===== Completeness check finished =====
[2024-01-24 12:44:54,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:44:54,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028775.1_ASM1602877v1_genomic.fna/markers.fasta)
[2024-01-24 12:44:54,033] [INFO] Task started: Blastn
[2024-01-24 12:44:54,033] [INFO] Running command: blastn -query GCF_016028775.1_ASM1602877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15bae058-bb80-4e20-a033-35072a8988d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028775.1_ASM1602877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:55,093] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:55,098] [INFO] Selected 7 target genomes.
[2024-01-24 12:44:55,098] [INFO] Target genome list was writen to GCF_016028775.1_ASM1602877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:44:55,111] [INFO] Task started: fastANI
[2024-01-24 12:44:55,111] [INFO] Running command: fastANI --query /var/lib/cwl/stga29b9ee9-ae3e-405c-9611-63d74150d56d/GCF_016028775.1_ASM1602877v1_genomic.fna.gz --refList GCF_016028775.1_ASM1602877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028775.1_ASM1602877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:44:59,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:59,242] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:44:59,243] [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_001679005.1	s__Moraxella nonliquefaciens	99.9605	742	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.13	98.18	0.96	0.92	5	conclusive
GCF_002027545.1	s__Moraxella lacunata	87.6508	568	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.28	95.16	0.88	0.84	9	-
GCF_000426885.1	s__Moraxella caprae	84.23	546	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	99.99	99.99	1.00	1.00	2	-
GCF_900453205.1	s__Moraxella lacunata_B	84.1901	557	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002027555.1	s__Moraxella equi	84.1039	515	780	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	84.0497	554	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.6695	98.79	98.38	0.94	0.91	3	-
GCF_001636015.1	s__Moraxella ovis	80.4969	220	780	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.978	97.95	96.93	0.90	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-24 12:44:59,245] [INFO] GTDB search result was written to GCF_016028775.1_ASM1602877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:44:59,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:44:59,248] [INFO] DFAST_QC result json was written to GCF_016028775.1_ASM1602877v1_genomic.fna/dqc_result.json
[2024-01-24 12:44:59,248] [INFO] DFAST_QC completed!
[2024-01-24 12:44:59,248] [INFO] Total running time: 0h0m48s