[2024-01-24 13:09:49,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,418] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference
[2024-01-24 13:09:50,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,652] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ebe786c-9855-464a-8b2f-3c59b3e82417/GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/cds.fna -a GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:01,146] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:01,147] [INFO] Task started: HMMsearch
[2024-01-24 13:10:01,147] [INFO] Running command: hmmsearch --tblout GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/reference_markers.hmm GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:01,431] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:01,432] [INFO] Found 6/6 markers.
[2024-01-24 13:10:01,466] [INFO] Query marker FASTA was written to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:10:01,466] [INFO] Task started: Blastn
[2024-01-24 13:10:01,467] [INFO] Running command: blastn -query GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/reference_markers.fasta -out GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:02,188] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:02,191] [INFO] Selected 26 target genomes.
[2024-01-24 13:10:02,192] [INFO] Target genome list was writen to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:10:02,262] [INFO] Task started: fastANI
[2024-01-24 13:10:02,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ebe786c-9855-464a-8b2f-3c59b3e82417/GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna.gz --refList GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:19,099] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:19,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:19,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:19,118] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:19,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:19,118] [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
Thiohalomonas denitrificans	strain=HLD2	GCA_900102855.1	415747	415747	type	True	100.0	1170	1173	95	conclusive
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	77.1804	195	1173	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.95	168	1173	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.8413	120	1173	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.789	105	1173	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.7666	155	1173	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	76.5751	107	1173	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.3566	66	1173	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.2897	69	1173	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	76.1738	89	1173	95	below_threshold
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	76.1287	50	1173	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.0804	90	1173	95	below_threshold
Halomonas zincidurans	strain=B6	GCA_000731955.1	1178777	1178777	type	True	76.0311	67	1173	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	75.9764	76	1173	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	75.9521	91	1173	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	75.952	61	1173	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	75.9084	77	1173	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.8811	90	1173	95	below_threshold
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	75.8497	76	1173	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	75.8318	90	1173	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	75.8042	84	1173	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	75.7773	74	1173	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.6372	77	1173	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	75.3522	68	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:19,120] [INFO] DFAST Taxonomy check result was written to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:19,120] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:19,120] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:19,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/checkm_data
[2024-01-24 13:10:19,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:19,162] [INFO] Task started: CheckM
[2024-01-24 13:10:19,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/checkm_input GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:53,305] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:53,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:53,329] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:53,329] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:53,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:53,330] [INFO] Task started: Blastn
[2024-01-24 13:10:53,331] [INFO] Running command: blastn -query GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa20e0c-41ba-45d8-b488-0e5cab5a1cbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:54,393] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:54,398] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:54,398] [INFO] Target genome list was writen to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:54,509] [INFO] Task started: fastANI
[2024-01-24 13:10:54,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ebe786c-9855-464a-8b2f-3c59b3e82417/GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna.gz --refList GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:07,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:07,736] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:07,736] [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_900102855.1	s__Thiohalomonas denitrificans	100.0	1170	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Thiohalomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016841685.1	s__Thiohalomonas denitrificans_A	88.7969	907	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Thiohalomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376325.1	s__Sulfurivermis sp002376325	77.3281	130	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	77.2035	222	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	77.194	194	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252455.1	s__SZUA-467 sp003252455	77.0972	155	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SZUA-467	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.9885	162	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	76.8604	119	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.6953	126	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.6843	154	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_007125455.1	s__SLDE01 sp007125455	76.5689	108	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__SLDE01	95.0	99.17	99.17	0.92	0.92	2	-
GCF_000801295.1	s__MONJU sp000801295	76.4191	123	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696465.1	s__J044 sp003696465	76.4073	86	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J044;f__J044;g__J044	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696905.1	s__MONJU sp003696905	76.3289	70	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__MONJU	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	76.1014	92	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	76.0109	100	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339665.1	s__Azotobacter chroococcum	75.8696	75	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_900109175.1	s__Pseudomonas_K linyingensis	75.8387	89	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007109405.1	s__VJOY01 sp007109405	75.7968	73	1173	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:07,738] [INFO] GTDB search result was written to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:07,738] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:07,746] [INFO] DFAST_QC result json was written to GCF_900102855.1_IMG-taxon_2593339163_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:11:07,746] [INFO] DFAST_QC completed!
[2024-01-24 13:11:07,746] [INFO] Total running time: 0h1m18s