[2024-01-24 13:48:42,808] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:42,811] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:42,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference
[2024-01-24 13:48:44,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,115] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,115] [INFO] Running command: gunzip -c /var/lib/cwl/stgbff02ac9-5dd7-4532-80ce-f53f000393fb/GCF_000613625.1_ASM61362v1_genomic.fna.gz | prodigal -d GCF_000613625.1_ASM61362v1_genomic.fna/cds.fna -a GCF_000613625.1_ASM61362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:58,507] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:58,508] [INFO] Task started: HMMsearch
[2024-01-24 13:48:58,508] [INFO] Running command: hmmsearch --tblout GCF_000613625.1_ASM61362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/reference_markers.hmm GCF_000613625.1_ASM61362v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:58,757] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:58,758] [INFO] Found 6/6 markers.
[2024-01-24 13:48:58,783] [INFO] Query marker FASTA was written to GCF_000613625.1_ASM61362v1_genomic.fna/markers.fasta
[2024-01-24 13:48:58,783] [INFO] Task started: Blastn
[2024-01-24 13:48:58,783] [INFO] Running command: blastn -query GCF_000613625.1_ASM61362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/reference_markers.fasta -out GCF_000613625.1_ASM61362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:59,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:59,382] [INFO] Selected 24 target genomes.
[2024-01-24 13:48:59,383] [INFO] Target genome list was writen to GCF_000613625.1_ASM61362v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:59,395] [INFO] Task started: fastANI
[2024-01-24 13:48:59,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff02ac9-5dd7-4532-80ce-f53f000393fb/GCF_000613625.1_ASM61362v1_genomic.fna.gz --refList GCF_000613625.1_ASM61362v1_genomic.fna/target_genomes.txt --output GCF_000613625.1_ASM61362v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:13,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:13,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:13,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:13,064] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:13,064] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:13,064] [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 marshii	strain=JCM 13450	GCA_000613625.1	189722	189722	type	True	100.0	795	799	95	conclusive
Prevotella marshii	strain=DSM 16973	GCA_000146675.1	189722	189722	type	True	99.9656	799	799	95	conclusive
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	80.9044	84	799	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	80.5104	80	799	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	80.4694	80	799	95	below_threshold
Prevotella aurantiaca	strain=JCM 15754	GCA_000614025.1	596085	596085	type	True	80.0235	68	799	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	79.5427	105	799	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	79.3553	104	799	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	78.9013	97	799	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	78.7088	114	799	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	78.5755	87	799	95	below_threshold
Prevotella loescheii	strain=JCM 12249	GCA_000613485.1	840	840	type	True	78.408	86	799	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	78.3652	64	799	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	78.3592	87	799	95	below_threshold
Prevotella shahii	strain=DSM 15611	GCA_003201715.1	228603	228603	type	True	78.1219	73	799	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:13,066] [INFO] DFAST Taxonomy check result was written to GCF_000613625.1_ASM61362v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:13,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:13,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:13,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/checkm_data
[2024-01-24 13:49:13,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:13,099] [INFO] Task started: CheckM
[2024-01-24 13:49:13,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613625.1_ASM61362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613625.1_ASM61362v1_genomic.fna/checkm_input GCF_000613625.1_ASM61362v1_genomic.fna/checkm_result
[2024-01-24 13:49:56,897] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:56,899] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,921] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:56,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:56,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613625.1_ASM61362v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:56,922] [INFO] Task started: Blastn
[2024-01-24 13:49:56,922] [INFO] Running command: blastn -query GCF_000613625.1_ASM61362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc47c37e8-a4cb-45c3-92d6-9d1c2009ea1d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613625.1_ASM61362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:57,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:57,817] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:57,818] [INFO] Target genome list was writen to GCF_000613625.1_ASM61362v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:57,848] [INFO] Task started: fastANI
[2024-01-24 13:49:57,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff02ac9-5dd7-4532-80ce-f53f000393fb/GCF_000613625.1_ASM61362v1_genomic.fna.gz --refList GCF_000613625.1_ASM61362v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613625.1_ASM61362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:12,069] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,083] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:12,084] [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_000146675.1	s__Prevotella marshii	99.9656	799	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.97	99.97	1.00	1.00	2	conclusive
GCF_018127805.1	s__Prevotella sp018127805	81.9434	106	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000184945.1	s__Prevotella buccae	78.7031	112	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	98.24	0.91	0.87	7	-
GCF_000378085.1	s__Prevotella loescheii	78.6656	85	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.09	95.73	0.96	0.93	5	-
GCF_013166515.1	s__Prevotella sp013166515	78.2912	60	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCF_001275135.1	s__Prevotella rara	78.1061	61	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_905196835.1	s__Prevotella stercoripullorum	77.7059	67	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_900545525.1	s__Prevotella sp900545525	77.1143	51	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCA_900315565.1	s__Prevotella sp900315565	76.3154	59	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.12	96.25	0.91	0.84	3	-
GCA_017557405.1	s__Prevotella sp017557405	76.2331	50	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373605.1	s__Prevotella sp905373605	76.1725	67	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767045.1	s__Prevotella sp902767045	76.0046	59	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.95	0.81	0.81	2	-
GCA_905235975.1	s__Prevotella sp905235975	75.7311	54	799	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 13:50:12,085] [INFO] GTDB search result was written to GCF_000613625.1_ASM61362v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:12,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:12,089] [INFO] DFAST_QC result json was written to GCF_000613625.1_ASM61362v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:12,090] [INFO] DFAST_QC completed!
[2024-01-24 13:50:12,090] [INFO] Total running time: 0h1m29s