[2024-01-24 14:06:29,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,671] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,671] [INFO] DQC Reference Directory: /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference
[2024-01-24 14:06:31,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,096] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg03fbe904-02c7-433e-aac1-338d54761ef2/GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/cds.fna -a GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:49,531] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:49,532] [INFO] Task started: HMMsearch
[2024-01-24 14:06:49,532] [INFO] Running command: hmmsearch --tblout GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/reference_markers.hmm GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:49,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:49,857] [INFO] Found 6/6 markers.
[2024-01-24 14:06:49,885] [INFO] Query marker FASTA was written to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:49,886] [INFO] Task started: Blastn
[2024-01-24 14:06:49,886] [INFO] Running command: blastn -query GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/reference_markers.fasta -out GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:50,522] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:50,526] [INFO] Selected 17 target genomes.
[2024-01-24 14:06:50,527] [INFO] Target genome list was writen to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:50,545] [INFO] Task started: fastANI
[2024-01-24 14:06:50,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg03fbe904-02c7-433e-aac1-338d54761ef2/GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna.gz --refList GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:59,693] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:59,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:59,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:59,708] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:59,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:59,709] [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
Prevotella oulorum	strain=ATCC 43324	GCA_900167385.1	28136	28136	type	True	100.0	910	916	95	conclusive
Prevotella oulorum	strain=JCM 14966	GCA_000613785.1	28136	28136	type	True	99.9087	847	916	95	conclusive
Prevotella saccharolytica	strain=JCM 17484	GCA_000614205.1	633701	633701	type	True	82.0978	83	916	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	80.9476	73	916	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	80.4364	71	916	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	80.3795	103	916	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	80.3283	214	916	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	80.2886	220	916	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	80.1662	115	916	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	80.1479	207	916	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.9651	201	916	95	below_threshold
Prevotella corporis	strain=DSM 18810	GCA_000430525.1	28128	28128	type	True	79.4966	70	916	95	below_threshold
Prevotella salivae	strain=DSM 15606	GCA_000185845.1	228604	228604	type	True	79.4307	173	916	95	below_threshold
Prevotella corporis	strain=JCM 8529	GCA_000613365.1	28128	28128	type	True	78.9206	64	916	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,710] [INFO] DFAST Taxonomy check result was written to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:59,711] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:59,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:59,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/checkm_data
[2024-01-24 14:06:59,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:59,741] [INFO] Task started: CheckM
[2024-01-24 14:06:59,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/checkm_input GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:51,521] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:51,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:51,543] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:51,543] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:51,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:51,544] [INFO] Task started: Blastn
[2024-01-24 14:07:51,544] [INFO] Running command: blastn -query GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg52618e57-b0bf-4329-9b8f-c293e169d21c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:52,371] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:52,376] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:52,376] [INFO] Target genome list was writen to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:52,398] [INFO] Task started: fastANI
[2024-01-24 14:07:52,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg03fbe904-02c7-433e-aac1-338d54761ef2/GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna.gz --refList GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:02,519] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:02,535] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:02,536] [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_000613785.1	s__Prevotella oulorum	99.9087	847	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	96.91	0.92	0.84	5	conclusive
GCF_000599605.1	s__Prevotella sp000599605	91.7302	717	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.66	96.63	0.93	0.92	3	-
GCF_000614025.1	s__Prevotella aurantiaca	81.0713	72	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.47	98.39	0.93	0.91	4	-
GCF_900637655.1	s__Prevotella oris	80.2958	216	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.96	97.06	0.90	0.82	10	-
GCF_000382385.1	s__Prevotella maculosa	80.185	206	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.13	97.00	0.93	0.87	4	-
GCF_000479005.1	s__Prevotella sp000479005	79.7125	96	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	96.42	0.92	0.87	3	-
GCF_000430525.1	s__Prevotella corporis	79.6108	67	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.63	97.78	0.92	0.87	4	-
GCF_000185845.1	s__Prevotella salivae	79.4348	172	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.60	96.70	0.94	0.87	27	-
GCF_000177075.1	s__Prevotella buccalis	78.5226	84	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.19	95.19	0.85	0.85	2	-
GCA_900199655.1	s__Prevotella sp900199655	78.226	86	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.91	99.91	0.98	0.98	2	-
GCA_900547085.1	s__Prevotella sp900547085	75.6457	53	916	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:02,539] [INFO] GTDB search result was written to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:02,540] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:02,546] [INFO] DFAST_QC result json was written to GCF_900167385.1_IMG-taxon_2585428083_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:08:02,546] [INFO] DFAST_QC completed!
[2024-01-24 14:08:02,547] [INFO] Total running time: 0h1m33s