[2023-06-28 13:49:38,170] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:49:38,173] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:49:38,173] [INFO] DQC Reference Directory: /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference
[2023-06-28 13:49:40,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:49:40,589] [INFO] Task started: Prodigal
[2023-06-28 13:49:40,589] [INFO] Running command: gunzip -c /var/lib/cwl/stgd252c5d2-5221-464f-830e-7558e39aebe8/GCA_944320795.1_BRZ_B_bin125_genomic.fna.gz | prodigal -d GCA_944320795.1_BRZ_B_bin125_genomic.fna/cds.fna -a GCA_944320795.1_BRZ_B_bin125_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:49:55,073] [INFO] Task succeeded: Prodigal
[2023-06-28 13:49:55,073] [INFO] Task started: HMMsearch
[2023-06-28 13:49:55,074] [INFO] Running command: hmmsearch --tblout GCA_944320795.1_BRZ_B_bin125_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/reference_markers.hmm GCA_944320795.1_BRZ_B_bin125_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:49:55,341] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:49:55,342] [INFO] Found 6/6 markers.
[2023-06-28 13:49:55,371] [INFO] Query marker FASTA was written to GCA_944320795.1_BRZ_B_bin125_genomic.fna/markers.fasta
[2023-06-28 13:49:55,372] [INFO] Task started: Blastn
[2023-06-28 13:49:55,372] [INFO] Running command: blastn -query GCA_944320795.1_BRZ_B_bin125_genomic.fna/markers.fasta -db /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/reference_markers.fasta -out GCA_944320795.1_BRZ_B_bin125_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:49:56,002] [INFO] Task succeeded: Blastn
[2023-06-28 13:49:56,007] [INFO] Selected 26 target genomes.
[2023-06-28 13:49:56,008] [INFO] Target genome list was writen to GCA_944320795.1_BRZ_B_bin125_genomic.fna/target_genomes.txt
[2023-06-28 13:49:56,017] [INFO] Task started: fastANI
[2023-06-28 13:49:56,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgd252c5d2-5221-464f-830e-7558e39aebe8/GCA_944320795.1_BRZ_B_bin125_genomic.fna.gz --refList GCA_944320795.1_BRZ_B_bin125_genomic.fna/target_genomes.txt --output GCA_944320795.1_BRZ_B_bin125_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:50:16,186] [INFO] Task succeeded: fastANI
[2023-06-28 13:50:16,187] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:50:16,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:50:16,206] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:50:16,207] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:50:16,207] [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
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.7717	106	914	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	77.7131	82	914	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	77.6258	132	914	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	77.5438	109	914	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	77.5208	109	914	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	77.4926	139	914	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	77.4496	141	914	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	77.4073	82	914	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.3015	67	914	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.0379	82	914	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	76.9447	73	914	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	76.9242	75	914	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	76.8888	80	914	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_000226135.2	674529	674529	type	True	76.8787	74	914	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	76.8449	89	914	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	76.821	89	914	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	76.6446	81	914	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	76.6074	87	914	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	76.5463	58	914	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:50:16,209] [INFO] DFAST Taxonomy check result was written to GCA_944320795.1_BRZ_B_bin125_genomic.fna/tc_result.tsv
[2023-06-28 13:50:16,209] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:50:16,210] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:50:16,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/checkm_data
[2023-06-28 13:50:16,211] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:50:16,253] [INFO] Task started: CheckM
[2023-06-28 13:50:16,254] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320795.1_BRZ_B_bin125_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320795.1_BRZ_B_bin125_genomic.fna/checkm_input GCA_944320795.1_BRZ_B_bin125_genomic.fna/checkm_result
[2023-06-28 13:51:01,359] [INFO] Task succeeded: CheckM
[2023-06-28 13:51:01,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:51:01,384] [INFO] ===== Completeness check finished =====
[2023-06-28 13:51:01,384] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:51:01,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320795.1_BRZ_B_bin125_genomic.fna/markers.fasta)
[2023-06-28 13:51:01,385] [INFO] Task started: Blastn
[2023-06-28 13:51:01,386] [INFO] Running command: blastn -query GCA_944320795.1_BRZ_B_bin125_genomic.fna/markers.fasta -db /var/lib/cwl/stg37890cf7-5011-47c8-bdfd-64c9c20d3850/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320795.1_BRZ_B_bin125_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:51:02,298] [INFO] Task succeeded: Blastn
[2023-06-28 13:51:02,303] [INFO] Selected 14 target genomes.
[2023-06-28 13:51:02,304] [INFO] Target genome list was writen to GCA_944320795.1_BRZ_B_bin125_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:51:02,313] [INFO] Task started: fastANI
[2023-06-28 13:51:02,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgd252c5d2-5221-464f-830e-7558e39aebe8/GCA_944320795.1_BRZ_B_bin125_genomic.fna.gz --refList GCA_944320795.1_BRZ_B_bin125_genomic.fna/target_genomes_gtdb.txt --output GCA_944320795.1_BRZ_B_bin125_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:51:12,131] [INFO] Task succeeded: fastANI
[2023-06-28 13:51:12,145] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:51:12,145] [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_018883665.1	s__Paraprevotella stercoravium	98.8553	672	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905215575.1	s__Paraprevotella sp905215575	88.5591	468	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477995.1	s__Paraprevotella sp003477995	86.9792	670	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.53	97.92	0.95	0.91	5	-
GCA_900546665.1	s__Paraprevotella stercorigallinarum	78.5737	150	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	99.24	99.20	0.80	0.74	3	-
GCA_017937925.1	s__Paraprevotella sp017937925	78.317	65	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.10	97.94	0.89	0.89	3	-
GCF_013618865.1	s__Phocaeicola sp900541515	77.6258	132	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCA_905214795.1	s__Paraprevotella sp905214795	77.6244	118	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760455.1	s__Paraprevotella sp900760455	77.4794	97	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
GCF_000157915.1	s__Phocaeicola coprophilus	77.4708	109	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_014385165.1	s__Bacteroides sp014385165	77.0338	50	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	0.99	0.99	2	-
GCA_910584955.1	s__Paraprevotella sp910584955	76.5271	86	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761785.1	s__Bacteroides sp900761785	76.0703	62	914	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:51:12,147] [INFO] GTDB search result was written to GCA_944320795.1_BRZ_B_bin125_genomic.fna/result_gtdb.tsv
[2023-06-28 13:51:12,148] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:51:12,152] [INFO] DFAST_QC result json was written to GCA_944320795.1_BRZ_B_bin125_genomic.fna/dqc_result.json
[2023-06-28 13:51:12,152] [INFO] DFAST_QC completed!
[2023-06-28 13:51:12,152] [INFO] Total running time: 0h1m34s