[2023-06-08 14:46:12,473] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:12,481] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:12,481] [INFO] DQC Reference Directory: /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference
[2023-06-08 14:46:13,976] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:13,977] [INFO] Task started: Prodigal
[2023-06-08 14:46:13,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c913edf-cd4d-48f3-b79b-126deea8d7de/GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:19,811] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:19,812] [INFO] Task started: HMMsearch
[2023-06-08 14:46:19,812] [INFO] Running command: hmmsearch --tblout GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/reference_markers.hmm GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:19,999] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:20,000] [INFO] Found 6/6 markers.
[2023-06-08 14:46:20,021] [INFO] Query marker FASTA was written to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 14:46:20,021] [INFO] Task started: Blastn
[2023-06-08 14:46:20,021] [INFO] Running command: blastn -query GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/reference_markers.fasta -out GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:20,668] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:20,672] [INFO] Selected 16 target genomes.
[2023-06-08 14:46:20,672] [INFO] Target genome list was writen to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:46:20,675] [INFO] Task started: fastANI
[2023-06-08 14:46:20,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c913edf-cd4d-48f3-b79b-126deea8d7de/GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:46:28,689] [INFO] Task succeeded: fastANI
[2023-06-08 14:46:28,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:46:28,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:46:28,700] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:46:28,700] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:46:28,700] [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 pluranimalium	strain=CCUG 54913	GCA_002014825.1	470453	470453	type	True	93.912	563	663	95	below_threshold
Moraxella porci	strain=CCUG 54912	GCA_002014855.1	1288392	1288392	type	True	85.4217	453	663	95	below_threshold
Moraxella cuniculi	strain=CCUG 2154	GCA_002015175.1	34061	34061	type	True	78.9703	290	663	95	below_threshold
Moraxella cuniculi	strain=DSM 21768	GCA_900156515.1	34061	34061	type	True	78.9543	292	663	95	below_threshold
Moraxella cuniculi	strain=NCTC10297	GCA_900637105.1	34061	34061	type	True	78.7176	277	663	95	below_threshold
Moraxella canis	strain=CCUG 8415A	GCA_002014965.1	90239	90239	type	True	78.6589	286	663	95	below_threshold
Moraxella caviae	strain=CCUG 355	GCA_002014985.1	34060	34060	type	True	78.2581	231	663	95	below_threshold
Moraxella catarrhalis	strain=CCUG 353	GCA_001632285.1	480	480	type	True	78.2447	211	663	95	below_threshold
Moraxella caviae	strain=NCTC10293	GCA_900453175.1	34060	34060	type	True	78.2352	243	663	95	below_threshold
Moraxella catarrhalis	strain=NCTC11020	GCA_900476075.1	480	480	type	True	78.1674	219	663	95	below_threshold
Moraxella oblonga	strain=NBRC 102422	GCA_001598275.1	200413	200413	type	True	77.0989	128	663	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:46:28,702] [INFO] DFAST Taxonomy check result was written to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:46:28,703] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:46:28,703] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:46:28,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/checkm_data
[2023-06-08 14:46:28,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:46:28,726] [INFO] Task started: CheckM
[2023-06-08 14:46:28,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 14:46:51,904] [INFO] Task succeeded: CheckM
[2023-06-08 14:46:51,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:46:51,921] [INFO] ===== Completeness check finished =====
[2023-06-08 14:46:51,921] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:46:51,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:46:51,922] [INFO] Task started: Blastn
[2023-06-08 14:46:51,922] [INFO] Running command: blastn -query GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd19be4a7-8c51-44b9-9a2d-9c444893c7a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:52,970] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:52,974] [INFO] Selected 9 target genomes.
[2023-06-08 14:46:52,974] [INFO] Target genome list was writen to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:46:52,978] [INFO] Task started: fastANI
[2023-06-08 14:46:52,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c913edf-cd4d-48f3-b79b-126deea8d7de/GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:46:56,939] [INFO] Task succeeded: fastANI
[2023-06-08 14:46:56,948] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:46:56,948] [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_002014825.1	s__Moraxella pluranimalium	93.912	563	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002014855.1	s__Moraxella porci	85.4365	452	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	96.21	96.21	0.92	0.92	2	-
GCF_900156515.1	s__Moraxella cuniculi	78.9664	290	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.10	98.21	0.93	0.87	3	-
GCF_001656295.1	s__Moraxella catarrhalis_C	78.7925	255	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.44	97.90	0.94	0.92	5	-
GCF_002014965.1	s__Moraxella canis	78.6589	286	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	97.14	96.86	0.93	0.92	4	-
GCF_001632285.1	s__Moraxella catarrhalis	78.2721	208	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	98.72	95.96	0.96	0.91	200	-
GCF_002014985.1	s__Moraxella caviae	78.2581	231	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	99.91	99.82	0.90	0.81	3	-
GCF_001598275.1	s__Moraxella oblonga	77.0785	129	663	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Moraxella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:46:56,950] [INFO] GTDB search result was written to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:46:56,951] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:46:56,954] [INFO] DFAST_QC result json was written to GCA_945873075.1_SRR15732366_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:46:56,954] [INFO] DFAST_QC completed!
[2023-06-08 14:46:56,954] [INFO] Total running time: 0h0m44s