[2024-01-24 12:47:28,131] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:28,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:28,133] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference
[2024-01-24 12:47:29,447] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,448] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,448] [INFO] Running command: gunzip -c /var/lib/cwl/stgac535fd0-b085-4bb6-b6a4-90f1f84cfdc8/GCF_019930665.1_ASM1993066v1_genomic.fna.gz | prodigal -d GCF_019930665.1_ASM1993066v1_genomic.fna/cds.fna -a GCF_019930665.1_ASM1993066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:56,356] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:56,356] [INFO] Task started: HMMsearch
[2024-01-24 12:47:56,356] [INFO] Running command: hmmsearch --tblout GCF_019930665.1_ASM1993066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/reference_markers.hmm GCF_019930665.1_ASM1993066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:56,687] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:56,688] [INFO] Found 6/6 markers.
[2024-01-24 12:47:56,733] [INFO] Query marker FASTA was written to GCF_019930665.1_ASM1993066v1_genomic.fna/markers.fasta
[2024-01-24 12:47:56,733] [INFO] Task started: Blastn
[2024-01-24 12:47:56,734] [INFO] Running command: blastn -query GCF_019930665.1_ASM1993066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/reference_markers.fasta -out GCF_019930665.1_ASM1993066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:57,434] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:57,438] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:57,438] [INFO] Target genome list was writen to GCF_019930665.1_ASM1993066v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:57,445] [INFO] Task started: fastANI
[2024-01-24 12:47:57,446] [INFO] Running command: fastANI --query /var/lib/cwl/stgac535fd0-b085-4bb6-b6a4-90f1f84cfdc8/GCF_019930665.1_ASM1993066v1_genomic.fna.gz --refList GCF_019930665.1_ASM1993066v1_genomic.fna/target_genomes.txt --output GCF_019930665.1_ASM1993066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:14,448] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:14,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:14,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:14,468] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:14,468] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:14,469] [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 nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	100.0	1890	1892	95	conclusive
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	81.2757	883	1892	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	80.0736	400	1892	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.9994	403	1892	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	79.9442	396	1892	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	79.7035	394	1892	95	below_threshold
Bacteroides fragilis	strain=NCTC 9343	GCA_900445515.1	817	817	type	True	79.5682	417	1892	95	below_threshold
Bacteroides fragilis	strain=FDAARGOS_1512	GCA_020097275.1	817	817	type	True	79.4269	420	1892	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	79.3018	438	1892	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	79.3006	460	1892	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.2575	434	1892	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	79.199	410	1892	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	79.1912	431	1892	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	79.1637	437	1892	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	79.1632	423	1892	95	below_threshold
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	79.0653	395	1892	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	79.0303	436	1892	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	78.3018	346	1892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:14,470] [INFO] DFAST Taxonomy check result was written to GCF_019930665.1_ASM1993066v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:14,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:14,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:14,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/checkm_data
[2024-01-24 12:48:14,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:14,527] [INFO] Task started: CheckM
[2024-01-24 12:48:14,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930665.1_ASM1993066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930665.1_ASM1993066v1_genomic.fna/checkm_input GCF_019930665.1_ASM1993066v1_genomic.fna/checkm_result
[2024-01-24 12:49:25,913] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:25,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:25,940] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:25,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:25,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930665.1_ASM1993066v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:25,942] [INFO] Task started: Blastn
[2024-01-24 12:49:25,942] [INFO] Running command: blastn -query GCF_019930665.1_ASM1993066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1029733-7617-4b01-81b0-abf034796e05/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930665.1_ASM1993066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:26,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:26,826] [INFO] Selected 13 target genomes.
[2024-01-24 12:49:26,826] [INFO] Target genome list was writen to GCF_019930665.1_ASM1993066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:26,859] [INFO] Task started: fastANI
[2024-01-24 12:49:26,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgac535fd0-b085-4bb6-b6a4-90f1f84cfdc8/GCF_019930665.1_ASM1993066v1_genomic.fna.gz --refList GCF_019930665.1_ASM1993066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930665.1_ASM1993066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:40,656] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:40,678] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:40,679] [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_000613465.1	s__Bacteroides nordii	99.9181	1803	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.55	98.11	0.85	0.80	13	conclusive
GCA_900762525.1	s__Bacteroides sp900762525	92.8533	1136	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381365.1	s__Bacteroides salyersiae	81.2656	879	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_001688725.2	s__Bacteroides caecimuris	80.1566	397	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_002849695.1	s__Bacteroides fragilis_A	79.8827	453	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.30	97.98	0.84	0.80	39	-
GCA_014385165.1	s__Bacteroides sp014385165	79.678	534	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000025985.1	s__Bacteroides fragilis	79.6101	412	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.01	98.63	0.88	0.79	194	-
GCF_000210075.1	s__Bacteroides xylanisolvens	79.2738	462	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_001314995.1	s__Bacteroides ovatus	79.1916	433	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_009193295.2	s__Bacteroides luhongzhouii	79.1693	424	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCF_002222615.2	s__Bacteroides caccae	79.12	398	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCA_905193145.1	s__Odoribacter sp905193145	78.5248	53	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Odoribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544675.1	s__Phocaeicola sp900544675	77.4925	104	1892	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:40,685] [INFO] GTDB search result was written to GCF_019930665.1_ASM1993066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:40,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:40,689] [INFO] DFAST_QC result json was written to GCF_019930665.1_ASM1993066v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:40,689] [INFO] DFAST_QC completed!
[2024-01-24 12:49:40,689] [INFO] Total running time: 0h2m13s