[2023-06-28 13:31:21,180] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:31:21,183] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:31:21,183] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference
[2023-06-28 13:31:22,307] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:31:22,308] [INFO] Task started: Prodigal
[2023-06-28 13:31:22,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg69478509-8729-4656-b7fd-ad8cc42e8aba/GCA_944319975.1_BRZ_AF_bin77_genomic.fna.gz | prodigal -d GCA_944319975.1_BRZ_AF_bin77_genomic.fna/cds.fna -a GCA_944319975.1_BRZ_AF_bin77_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:31:36,962] [INFO] Task succeeded: Prodigal
[2023-06-28 13:31:36,962] [INFO] Task started: HMMsearch
[2023-06-28 13:31:36,962] [INFO] Running command: hmmsearch --tblout GCA_944319975.1_BRZ_AF_bin77_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/reference_markers.hmm GCA_944319975.1_BRZ_AF_bin77_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:31:37,162] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:31:37,163] [INFO] Found 6/6 markers.
[2023-06-28 13:31:37,188] [INFO] Query marker FASTA was written to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/markers.fasta
[2023-06-28 13:31:37,188] [INFO] Task started: Blastn
[2023-06-28 13:31:37,188] [INFO] Running command: blastn -query GCA_944319975.1_BRZ_AF_bin77_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/reference_markers.fasta -out GCA_944319975.1_BRZ_AF_bin77_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:31:37,736] [INFO] Task succeeded: Blastn
[2023-06-28 13:31:37,740] [INFO] Selected 26 target genomes.
[2023-06-28 13:31:37,740] [INFO] Target genome list was writen to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/target_genomes.txt
[2023-06-28 13:31:37,741] [INFO] Task started: fastANI
[2023-06-28 13:31:37,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg69478509-8729-4656-b7fd-ad8cc42e8aba/GCA_944319975.1_BRZ_AF_bin77_genomic.fna.gz --refList GCA_944319975.1_BRZ_AF_bin77_genomic.fna/target_genomes.txt --output GCA_944319975.1_BRZ_AF_bin77_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:31:50,653] [INFO] Task succeeded: fastANI
[2023-06-28 13:31:50,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:31:50,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:31:50,664] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:31:50,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:31:50,664] [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 lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.8805	129	978	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.529	126	978	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.4847	61	978	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.2965	127	978	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.237	115	978	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	77.0461	123	978	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	77.0231	121	978	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.9843	68	978	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9334	106	978	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.9136	66	978	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.8858	65	978	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.7701	130	978	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.6264	140	978	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.6175	136	978	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.433	72	978	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.2654	108	978	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:31:50,666] [INFO] DFAST Taxonomy check result was written to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/tc_result.tsv
[2023-06-28 13:31:50,666] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:31:50,666] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:31:50,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/checkm_data
[2023-06-28 13:31:50,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:31:50,697] [INFO] Task started: CheckM
[2023-06-28 13:31:50,697] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944319975.1_BRZ_AF_bin77_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944319975.1_BRZ_AF_bin77_genomic.fna/checkm_input GCA_944319975.1_BRZ_AF_bin77_genomic.fna/checkm_result
[2023-06-28 13:32:31,909] [INFO] Task succeeded: CheckM
[2023-06-28 13:32:31,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:32:31,927] [INFO] ===== Completeness check finished =====
[2023-06-28 13:32:31,927] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:32:31,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944319975.1_BRZ_AF_bin77_genomic.fna/markers.fasta)
[2023-06-28 13:32:31,928] [INFO] Task started: Blastn
[2023-06-28 13:32:31,928] [INFO] Running command: blastn -query GCA_944319975.1_BRZ_AF_bin77_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f4b5a63-f076-4a63-bac6-10c8814b52ff/dqc_reference/reference_markers_gtdb.fasta -out GCA_944319975.1_BRZ_AF_bin77_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:32:32,786] [INFO] Task succeeded: Blastn
[2023-06-28 13:32:32,789] [INFO] Selected 14 target genomes.
[2023-06-28 13:32:32,789] [INFO] Target genome list was writen to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:32:32,792] [INFO] Task started: fastANI
[2023-06-28 13:32:32,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg69478509-8729-4656-b7fd-ad8cc42e8aba/GCA_944319975.1_BRZ_AF_bin77_genomic.fna.gz --refList GCA_944319975.1_BRZ_AF_bin77_genomic.fna/target_genomes_gtdb.txt --output GCA_944319975.1_BRZ_AF_bin77_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:32:41,174] [INFO] Task succeeded: fastANI
[2023-06-28 13:32:41,183] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:32:41,183] [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
GCA_905196835.1	s__Prevotella stercoripullorum	96.1521	818	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	conclusive
GCA_900554545.1	s__Prevotella sp900554545	85.0577	508	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.89	0.89	0.88	3	-
GCA_900551055.1	s__Prevotella sp900551055	84.0182	610	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.16	98.15	0.84	0.84	3	-
GCA_905211345.1	s__Prevotella sp905211345	83.4411	305	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899855.1	s__Prevotella sp000436595	80.8061	449	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCA_900550365.1	s__Prevotella sp900550365	80.4518	393	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433175.1	s__Prevotella sp000433175	80.1751	342	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCA_900545525.1	s__Prevotella sp900545525	77.5734	154	978	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	77.3538	164	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_905216025.1	s__Prevotella sp905216025	77.2323	190	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_004557285.1	s__Prevotella sp004557285	77.1436	151	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_004558865.1	s__Prevotella sp004558865	77.0777	113	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770845.1	s__Prevotella sp900770845	76.6456	117	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016901395.1	s__Prevotella sp016901395	76.4763	95	978	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:32:41,219] [INFO] GTDB search result was written to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/result_gtdb.tsv
[2023-06-28 13:32:41,221] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:32:41,224] [INFO] DFAST_QC result json was written to GCA_944319975.1_BRZ_AF_bin77_genomic.fna/dqc_result.json
[2023-06-28 13:32:41,224] [INFO] DFAST_QC completed!
[2023-06-28 13:32:41,224] [INFO] Total running time: 0h1m20s