[2023-06-08 05:13:50,837] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:13:50,847] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:13:50,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference
[2023-06-08 05:13:52,831] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:13:52,832] [INFO] Task started: Prodigal
[2023-06-08 05:13:52,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3db5382-69a3-4243-8648-c43684c8d7db/GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:14:05,609] [INFO] Task succeeded: Prodigal
[2023-06-08 05:14:05,609] [INFO] Task started: HMMsearch
[2023-06-08 05:14:05,610] [INFO] Running command: hmmsearch --tblout GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/reference_markers.hmm GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:14:05,981] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:14:05,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3db5382-69a3-4243-8648-c43684c8d7db/GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 05:14:06,028] [INFO] Query marker FASTA was written to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:14:06,029] [INFO] Task started: Blastn
[2023-06-08 05:14:06,029] [INFO] Running command: blastn -query GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/reference_markers.fasta -out GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:06,898] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:06,907] [INFO] Selected 27 target genomes.
[2023-06-08 05:14:06,907] [INFO] Target genome list was writen to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:14:06,915] [INFO] Task started: fastANI
[2023-06-08 05:14:06,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3db5382-69a3-4243-8648-c43684c8d7db/GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:14:25,925] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:25,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:14:25,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:14:25,951] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:14:25,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:14:25,951] [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
Bacteroides fragilis	strain=NCTC 9343	GCA_000025985.1	817	817	type	True	77.0875	75	945	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	76.9892	77	945	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	76.9892	77	945	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	76.9651	143	945	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	76.9238	80	945	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	76.8375	102	945	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	76.7375	102	945	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	76.7085	101	945	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	76.5248	105	945	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	76.5218	100	945	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	76.5201	99	945	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	76.5188	99	945	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	76.5104	108	945	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	76.5056	107	945	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	76.5054	107	945	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	76.4804	101	945	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_002959695.1	818	818	type	True	76.4791	101	945	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	76.4739	107	945	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	76.4079	118	945	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	76.3433	120	945	95	below_threshold
Bacteroides finegoldii	strain=DSM 17565	GCA_000156195.1	338188	338188	suspected-type	True	76.3281	106	945	95	below_threshold
Bacteroides faecichinchillae	strain=JCM 17102	GCA_000614145.1	871325	871325	type	True	76.304	120	945	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	76.2382	114	945	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	76.1383	110	945	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	76.1162	113	945	95	below_threshold
Bacteroides ihuae	strain=Marseille-P2824	GCA_900104585.1	1852362	1852362	type	True	75.9053	79	945	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:14:25,953] [INFO] DFAST Taxonomy check result was written to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:14:25,954] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:14:25,954] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:14:25,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/checkm_data
[2023-06-08 05:14:25,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:14:25,993] [INFO] Task started: CheckM
[2023-06-08 05:14:25,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:15:06,185] [INFO] Task succeeded: CheckM
[2023-06-08 05:15:06,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:15:06,208] [INFO] ===== Completeness check finished =====
[2023-06-08 05:15:06,208] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:15:06,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:15:06,209] [INFO] Task started: Blastn
[2023-06-08 05:15:06,209] [INFO] Running command: blastn -query GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c492ac-07dc-47c2-9a72-45bcbec2aefc/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:07,035] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:07,040] [INFO] Selected 26 target genomes.
[2023-06-08 05:15:07,041] [INFO] Target genome list was writen to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:15:07,052] [INFO] Task started: fastANI
[2023-06-08 05:15:07,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3db5382-69a3-4243-8648-c43684c8d7db/GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:15:24,632] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:24,651] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 05:15:24,652] [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_002471185.1	s__Bacteroides sp002471185	78.4634	166	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471195.1	s__Bacteroides sp002471195	77.7795	216	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025985.1	s__Bacteroides fragilis	77.0307	73	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCA_000613465.1	s__Bacteroides nordii	77.0157	135	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	-
GCF_002849695.1	s__Bacteroides fragilis_A	76.9325	79	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCF_000499785.1	s__Bacteroides neonati	76.7778	100	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001314995.1	s__Bacteroides ovatus	76.6403	99	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCA_900547205.1	s__Bacteroides sp900547205	76.6312	96	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.95	0.95	2	-
GCA_902362375.1	s__Bacteroides sp902362375	76.5985	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCA_014385165.1	s__Bacteroides sp014385165	76.5572	89	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCA_900762525.1	s__Bacteroides sp900762525	76.5542	105	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001688725.2	s__Bacteroides caecimuris	76.4995	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	76.4983	98	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_000210075.1	s__Bacteroides xylanisolvens	76.4538	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_009193295.2	s__Bacteroides luhongzhouii	76.4098	115	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_000156195.1	s__Bacteroides finegoldii	76.3053	105	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCF_014750685.1	s__Bacteroides sp014750685	76.2787	104	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614145.1	s__Bacteroides faecichinchillae	76.2515	116	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.89	99.80	0.96	0.92	3	-
GCF_900128905.1	s__Bacteroides_G luti	76.1875	87	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	76.1866	112	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCA_900552645.1	s__Phocaeicola sp900552645	76.0744	54	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104585.1	s__Bacteroides ihuae	75.8469	78	945	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:15:24,654] [INFO] GTDB search result was written to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:15:24,654] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:15:24,659] [INFO] DFAST_QC result json was written to GCA_947074345.1_SRR7610133_bin.2_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:15:24,659] [INFO] DFAST_QC completed!
[2023-06-08 05:15:24,660] [INFO] Total running time: 0h1m34s