[2023-06-19 10:30:22,713] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:30:22,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:30:22,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference
[2023-06-19 10:30:24,211] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:30:24,212] [INFO] Task started: Prodigal
[2023-06-19 10:30:24,212] [INFO] Running command: gunzip -c /var/lib/cwl/stg2eba0728-9731-4c74-9d16-07f6e365e8b0/GCA_018372025.1_ASM1837202v1_genomic.fna.gz | prodigal -d GCA_018372025.1_ASM1837202v1_genomic.fna/cds.fna -a GCA_018372025.1_ASM1837202v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:30:40,746] [INFO] Task succeeded: Prodigal
[2023-06-19 10:30:40,746] [INFO] Task started: HMMsearch
[2023-06-19 10:30:40,746] [INFO] Running command: hmmsearch --tblout GCA_018372025.1_ASM1837202v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/reference_markers.hmm GCA_018372025.1_ASM1837202v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:30:41,014] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:30:41,015] [INFO] Found 6/6 markers.
[2023-06-19 10:30:41,053] [INFO] Query marker FASTA was written to GCA_018372025.1_ASM1837202v1_genomic.fna/markers.fasta
[2023-06-19 10:30:41,054] [INFO] Task started: Blastn
[2023-06-19 10:30:41,054] [INFO] Running command: blastn -query GCA_018372025.1_ASM1837202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/reference_markers.fasta -out GCA_018372025.1_ASM1837202v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:30:41,709] [INFO] Task succeeded: Blastn
[2023-06-19 10:30:41,713] [INFO] Selected 26 target genomes.
[2023-06-19 10:30:41,714] [INFO] Target genome list was writen to GCA_018372025.1_ASM1837202v1_genomic.fna/target_genomes.txt
[2023-06-19 10:30:41,716] [INFO] Task started: fastANI
[2023-06-19 10:30:41,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eba0728-9731-4c74-9d16-07f6e365e8b0/GCA_018372025.1_ASM1837202v1_genomic.fna.gz --refList GCA_018372025.1_ASM1837202v1_genomic.fna/target_genomes.txt --output GCA_018372025.1_ASM1837202v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:30:56,031] [INFO] Task succeeded: fastANI
[2023-06-19 10:30:56,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:30:56,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:30:56,043] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:30:56,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 10:30:56,043] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.9351	171	1055	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.7935	135	1055	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.3819	163	1055	95	below_threshold
Prevotella phocaeensis	strain=SN19	GCA_900065875.1	1776388	1776388	type	True	77.3268	56	1055	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.2847	125	1055	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.2231	55	1055	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	77.0757	56	1055	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	77.0529	54	1055	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.9883	77	1055	95	below_threshold
Prevotella paludivivens	strain=JCM 13650	GCA_000613605.1	185294	185294	type	True	76.896	58	1055	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6938	93	1055	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	76.6315	68	1055	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 10:30:56,045] [INFO] DFAST Taxonomy check result was written to GCA_018372025.1_ASM1837202v1_genomic.fna/tc_result.tsv
[2023-06-19 10:30:56,052] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:30:56,052] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:30:56,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/checkm_data
[2023-06-19 10:30:56,054] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:30:56,094] [INFO] Task started: CheckM
[2023-06-19 10:30:56,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018372025.1_ASM1837202v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018372025.1_ASM1837202v1_genomic.fna/checkm_input GCA_018372025.1_ASM1837202v1_genomic.fna/checkm_result
[2023-06-19 10:31:44,787] [INFO] Task succeeded: CheckM
[2023-06-19 10:31:44,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 10:31:44,809] [INFO] ===== Completeness check finished =====
[2023-06-19 10:31:44,809] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:31:44,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018372025.1_ASM1837202v1_genomic.fna/markers.fasta)
[2023-06-19 10:31:44,810] [INFO] Task started: Blastn
[2023-06-19 10:31:44,810] [INFO] Running command: blastn -query GCA_018372025.1_ASM1837202v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6b13682-8c1d-402d-aa5a-31f6f30603f7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018372025.1_ASM1837202v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:31:45,716] [INFO] Task succeeded: Blastn
[2023-06-19 10:31:45,721] [INFO] Selected 19 target genomes.
[2023-06-19 10:31:45,721] [INFO] Target genome list was writen to GCA_018372025.1_ASM1837202v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:31:45,761] [INFO] Task started: fastANI
[2023-06-19 10:31:45,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg2eba0728-9731-4c74-9d16-07f6e365e8b0/GCA_018372025.1_ASM1837202v1_genomic.fna.gz --refList GCA_018372025.1_ASM1837202v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018372025.1_ASM1837202v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:31:55,084] [INFO] Task succeeded: fastANI
[2023-06-19 10:31:55,100] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:31:55,100] [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_001275135.1	s__Prevotella rara	97.8637	938	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	conclusive
GCA_905214625.1	s__Prevotella sp905214625	89.7448	562	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436695.1	s__Prevotella sp000436695	85.8873	681	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.24	0.85	0.83	3	-
GCA_000433175.1	s__Prevotella sp000433175	79.9947	313	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCA_900550365.1	s__Prevotella sp900550365	79.0385	273	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905211345.1	s__Prevotella sp905211345	78.495	190	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551055.1	s__Prevotella sp900551055	78.1257	268	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.16	98.15	0.84	0.84	3	-
GCA_900768785.1	s__Prevotella sp900768785	77.658	74	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	77.6019	200	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_013166515.1	s__Prevotella sp013166515	77.53	187	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_900772835.1	s__Prevotella sp900772835	77.2307	142	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373185.1	s__Prevotella paludivivens	77.0757	56	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.98	99.98	0.99	0.99	2	-
GCA_900314985.1	s__Prevotella sp900314985	76.8351	77	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_900315075.1	s__Prevotella sp900315075	76.7494	62	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
GCA_017444365.1	s__Prevotella sp017444365	76.003	57	1055	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:31:55,102] [INFO] GTDB search result was written to GCA_018372025.1_ASM1837202v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:31:55,103] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:31:55,106] [INFO] DFAST_QC result json was written to GCA_018372025.1_ASM1837202v1_genomic.fna/dqc_result.json
[2023-06-19 10:31:55,107] [INFO] DFAST_QC completed!
[2023-06-19 10:31:55,107] [INFO] Total running time: 0h1m32s