[2024-01-24 15:10:48,140] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,142] [INFO] DQC Reference Directory: /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference
[2024-01-24 15:10:51,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,752] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg3459b50c-53a6-4fd5-b6da-79eea30c1895/GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/cds.fna -a GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:05,682] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:05,682] [INFO] Task started: HMMsearch
[2024-01-24 15:11:05,682] [INFO] Running command: hmmsearch --tblout GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/reference_markers.hmm GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:05,986] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:05,988] [INFO] Found 6/6 markers.
[2024-01-24 15:11:06,025] [INFO] Query marker FASTA was written to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 15:11:06,025] [INFO] Task started: Blastn
[2024-01-24 15:11:06,025] [INFO] Running command: blastn -query GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/reference_markers.fasta -out GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,774] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,779] [INFO] Selected 22 target genomes.
[2024-01-24 15:11:06,779] [INFO] Target genome list was writen to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 15:11:06,792] [INFO] Task started: fastANI
[2024-01-24 15:11:06,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg3459b50c-53a6-4fd5-b6da-79eea30c1895/GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna.gz --refList GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:21,248] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:21,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:21,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:21,324] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:21,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:21,325] [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
Salegentibacter flavus	strain=DSM 17794	GCA_900115145.1	287099	287099	type	True	100.0	1196	1201	95	conclusive
Salegentibacter sediminis	strain=K5023	GCA_002078605.1	1930251	1930251	type	True	85.8905	887	1201	95	below_threshold
Salegentibacter tibetensis	strain=JZCK2	GCA_020164485.1	2873600	2873600	type	True	79.3194	437	1201	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	78.9069	414	1201	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	78.7526	400	1201	95	below_threshold
Salegentibacter salarius	strain=KCTC 12974	GCA_002833385.1	435906	435906	type	True	78.5946	361	1201	95	below_threshold
Salegentibacter salarius	strain=DSM 23401	GCA_900168265.1	435906	435906	type	True	78.5547	366	1201	95	below_threshold
Salegentibacter salegens	strain=DSM 5424	GCA_003001895.1	143223	143223	type	True	78.476	395	1201	95	below_threshold
Salegentibacter salegens	strain=ACAM 48	GCA_900142975.1	143223	143223	type	True	78.436	404	1201	95	below_threshold
Gramella forsetii	strain=KT0803	GCA_000060345.1	411153	411153	type	True	77.8763	209	1201	95	below_threshold
Gramella forsetii	strain=CGMCC 1.15422	GCA_014642775.1	411153	411153	type	True	77.814	203	1201	95	below_threshold
Gramella lutea	strain=YJ019	GCA_022489035.1	1607951	1607951	type	True	77.5423	163	1201	95	below_threshold
Zunongwangia profunda	strain=SMA-87	GCA_000023465.1	398743	398743	type	True	77.515	182	1201	95	below_threshold
Gramella sabulilitoris	strain=HSMS-1	GCA_007050985.1	2583991	2583991	type	True	77.5096	169	1201	95	below_threshold
Zunongwangia mangrovi	strain=DSM 24499	GCA_900112105.1	1334022	1334022	type	True	77.3537	176	1201	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	77.2992	185	1201	95	below_threshold
Gramella crocea	strain=YB25	GCA_022410465.1	2904124	2904124	type	True	77.2238	203	1201	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.4839	56	1201	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.3657	50	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:21,327] [INFO] DFAST Taxonomy check result was written to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 15:11:21,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:21,330] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:21,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/checkm_data
[2024-01-24 15:11:21,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:21,379] [INFO] Task started: CheckM
[2024-01-24 15:11:21,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/checkm_input GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 15:12:04,194] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:04,195] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:04,217] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:04,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:04,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 15:12:04,218] [INFO] Task started: Blastn
[2024-01-24 15:12:04,218] [INFO] Running command: blastn -query GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg89c4c3e3-f853-4d66-968e-c44d32ca3e72/dqc_reference/reference_markers_gtdb.fasta -out GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:05,095] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:05,099] [INFO] Selected 16 target genomes.
[2024-01-24 15:12:05,099] [INFO] Target genome list was writen to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:05,113] [INFO] Task started: fastANI
[2024-01-24 15:12:05,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg3459b50c-53a6-4fd5-b6da-79eea30c1895/GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna.gz --refList GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:16,654] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:16,668] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:16,668] [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_900115145.1	s__Salegentibacter flavus	100.0	1196	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002078605.1	s__Salegentibacter sediminis	85.8775	888	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	78.7437	401	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_004362395.1	s__Salegentibacter sp004362395	78.6297	348	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168265.1	s__Salegentibacter salarius	78.5547	366	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	99.99	1.00	0.99	3	-
GCF_900168115.1	s__Salegentibacter salinarum	78.4905	400	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142975.1	s__Salegentibacter salegens	78.4529	401	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017795085.1	s__Salegentibacter sp017795085	78.1473	345	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016236915.1	s__Salegentibacter maritimus	78.1344	323	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	98.25	98.21	0.91	0.91	3	-
GCF_000060345.1	s__Gramella forsetii	77.8763	209	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007050985.1	s__Gramella sabulilitoris	77.5096	169	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gramella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023465.1	s__Zunongwangia profunda	77.501	183	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	99.17	98.44	0.93	0.80	11	-
GCF_900112105.1	s__Zunongwangia mangrovi	77.3847	174	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649785.1	s__Gillisia sp016649785	76.6808	119	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997135.1	s__Aequorivita lipolytica	76.4839	56	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900489465.1	s__Aequorivita sp900489465	76.3637	56	1201	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:16,670] [INFO] GTDB search result was written to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:16,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:16,677] [INFO] DFAST_QC result json was written to GCF_900115145.1_IMG-taxon_2599185209_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 15:12:16,677] [INFO] DFAST_QC completed!
[2024-01-24 15:12:16,677] [INFO] Total running time: 0h1m29s