[2024-01-25 19:42:20,665] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:20,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:20,666] [INFO] DQC Reference Directory: /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference
[2024-01-25 19:42:21,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:21,769] [INFO] Task started: Prodigal
[2024-01-25 19:42:21,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a1a7a5d-5967-47ac-a45d-58c0bb8d70f4/GCF_021295095.1_ASM2129509v1_genomic.fna.gz | prodigal -d GCF_021295095.1_ASM2129509v1_genomic.fna/cds.fna -a GCF_021295095.1_ASM2129509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:33,029] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:33,029] [INFO] Task started: HMMsearch
[2024-01-25 19:42:33,029] [INFO] Running command: hmmsearch --tblout GCF_021295095.1_ASM2129509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/reference_markers.hmm GCF_021295095.1_ASM2129509v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:33,279] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:33,280] [INFO] Found 6/6 markers.
[2024-01-25 19:42:33,308] [INFO] Query marker FASTA was written to GCF_021295095.1_ASM2129509v1_genomic.fna/markers.fasta
[2024-01-25 19:42:33,308] [INFO] Task started: Blastn
[2024-01-25 19:42:33,308] [INFO] Running command: blastn -query GCF_021295095.1_ASM2129509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/reference_markers.fasta -out GCF_021295095.1_ASM2129509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:33,864] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:33,867] [INFO] Selected 28 target genomes.
[2024-01-25 19:42:33,867] [INFO] Target genome list was writen to GCF_021295095.1_ASM2129509v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:33,884] [INFO] Task started: fastANI
[2024-01-25 19:42:33,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a1a7a5d-5967-47ac-a45d-58c0bb8d70f4/GCF_021295095.1_ASM2129509v1_genomic.fna.gz --refList GCF_021295095.1_ASM2129509v1_genomic.fna/target_genomes.txt --output GCF_021295095.1_ASM2129509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:50,155] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:50,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:50,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:50,168] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:42:50,168] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:42:50,168] [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
Phocaeicola abscessus	strain=CCUG 55929	GCA_000312445.1	555313	555313	type	True	78.0103	101	968	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	77.1918	51	968	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.0999	56	968	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_002959715.1	47678	47678	suspected-type	True	77.0898	53	968	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	77.0225	86	968	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	77.0025	86	968	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_000169015.1	47678	47678	suspected-type	True	76.9499	52	968	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	76.8949	51	968	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	76.8538	52	968	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	76.8353	50	968	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	76.8165	64	968	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	76.7914	51	968	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	76.7373	51	968	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	76.6931	52	968	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	76.6931	52	968	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	76.6763	80	968	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_000011065.1	818	818	type	True	76.6042	51	968	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	76.3511	51	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:50,183] [INFO] DFAST Taxonomy check result was written to GCF_021295095.1_ASM2129509v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:50,186] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:50,186] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:50,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/checkm_data
[2024-01-25 19:42:50,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:50,223] [INFO] Task started: CheckM
[2024-01-25 19:42:50,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021295095.1_ASM2129509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021295095.1_ASM2129509v1_genomic.fna/checkm_input GCF_021295095.1_ASM2129509v1_genomic.fna/checkm_result
[2024-01-25 19:43:24,728] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:24,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:24,746] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:24,746] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:24,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021295095.1_ASM2129509v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:24,747] [INFO] Task started: Blastn
[2024-01-25 19:43:24,747] [INFO] Running command: blastn -query GCF_021295095.1_ASM2129509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8dac2fc-9854-45ec-b694-8a4da6f4010b/dqc_reference/reference_markers_gtdb.fasta -out GCF_021295095.1_ASM2129509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:25,578] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:25,581] [INFO] Selected 31 target genomes.
[2024-01-25 19:43:25,582] [INFO] Target genome list was writen to GCF_021295095.1_ASM2129509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:25,629] [INFO] Task started: fastANI
[2024-01-25 19:43:25,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a1a7a5d-5967-47ac-a45d-58c0bb8d70f4/GCF_021295095.1_ASM2129509v1_genomic.fna.gz --refList GCF_021295095.1_ASM2129509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021295095.1_ASM2129509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:42,375] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:42,382] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:43:42,382] [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_000312445.1	s__Phocaeicola abscessus	78.0465	100	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.49	99.45	0.95	0.95	3	-
GCF_002222615.2	s__Bacteroides caccae	77.1939	51	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	77.0892	51	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000382445.1	s__Phocaeicola massiliensis	77.0536	85	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCF_000187895.1	s__Phocaeicola plebeius	77.0531	57	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	77.0477	52	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCA_902779535.1	s__Phocaeicola sp902779535	76.9096	104	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.97	97.63	0.83	0.71	5	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	76.6042	51	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_000154845.1	s__Phocaeicola coprocola	76.3581	81	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCA_900760795.1	s__Phocaeicola sp900760795	76.2209	62	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542985.1	s__Phocaeicola sp900542985	76.1533	50	968	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:42,385] [INFO] GTDB search result was written to GCF_021295095.1_ASM2129509v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:42,385] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:42,388] [INFO] DFAST_QC result json was written to GCF_021295095.1_ASM2129509v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:42,388] [INFO] DFAST_QC completed!
[2024-01-25 19:43:42,388] [INFO] Total running time: 0h1m22s