[2024-01-24 14:39:15,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,429] [INFO] DQC Reference Directory: /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference
[2024-01-24 14:39:16,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,806] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,806] [INFO] Running command: gunzip -c /var/lib/cwl/stgade841e1-fb1b-4486-937a-392ec9dd9553/GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/cds.fna -a GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:38,885] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:38,886] [INFO] Task started: HMMsearch
[2024-01-24 14:39:38,886] [INFO] Running command: hmmsearch --tblout GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/reference_markers.hmm GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:39,143] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:39,147] [INFO] Found 6/6 markers.
[2024-01-24 14:39:39,181] [INFO] Query marker FASTA was written to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:39:39,181] [INFO] Task started: Blastn
[2024-01-24 14:39:39,181] [INFO] Running command: blastn -query GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/reference_markers.fasta -out GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:39,858] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:39,861] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:39,862] [INFO] Target genome list was writen to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:39:39,869] [INFO] Task started: fastANI
[2024-01-24 14:39:39,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgade841e1-fb1b-4486-937a-392ec9dd9553/GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna.gz --refList GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:53,383] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:53,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:53,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:53,397] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:53,397] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:53,397] [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
Muricauda flava	strain=DSM 22638	GCA_900129665.1	570519	570519	type	True	100.0	1271	1271	95	conclusive
Muricauda algicola	strain=AsT0115	GCA_005937185.1	2583815	2583815	type	True	79.081	523	1271	95	below_threshold
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	78.4329	380	1271	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	78.3885	349	1271	95	below_threshold
Muricauda olearia	strain=CL-SS4	GCA_009184425.1	552546	552546	type	True	78.0867	299	1271	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	78.0533	329	1271	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	77.9756	235	1271	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	77.9252	257	1271	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	77.8658	349	1271	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	77.8372	265	1271	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	77.833	266	1271	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	77.7679	239	1271	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	77.752	295	1271	95	below_threshold
Muricauda ruestringensis	strain=DSM 13258	GCA_000224085.1	111501	111501	type	True	77.7349	256	1271	95	below_threshold
Muricauda sediminis	strain=40Bstr401	GCA_010500845.1	2696468	2696468	type	True	77.5957	243	1271	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	77.3389	256	1271	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:53,399] [INFO] DFAST Taxonomy check result was written to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:39:53,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:53,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:53,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/checkm_data
[2024-01-24 14:39:53,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:53,444] [INFO] Task started: CheckM
[2024-01-24 14:39:53,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/checkm_input GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:40:49,920] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:49,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:49,940] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:49,941] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:49,941] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:40:49,942] [INFO] Task started: Blastn
[2024-01-24 14:40:49,942] [INFO] Running command: blastn -query GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgda3b8563-6008-4474-9635-3318ed731012/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:50,735] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:50,740] [INFO] Selected 20 target genomes.
[2024-01-24 14:40:50,740] [INFO] Target genome list was writen to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:50,775] [INFO] Task started: fastANI
[2024-01-24 14:40:50,775] [INFO] Running command: fastANI --query /var/lib/cwl/stgade841e1-fb1b-4486-937a-392ec9dd9553/GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna.gz --refList GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:04,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:04,842] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:04,842] [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_900129665.1	s__Muricauda flava	100.0	1271	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005937185.1	s__Muricauda algicola	79.081	523	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	78.4329	380	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804315.1	s__Muricauda sp004804315	78.3994	348	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698935.1	s__Muricauda sp014698935	78.2224	387	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184425.1	s__Muricauda olearia	78.0982	298	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.52	96.52	0.87	0.87	2	-
GCF_000745185.1	s__Muricauda sp000745185	78.0706	309	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382275.1	s__Muricauda nanhaiensis	78.0533	329	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	78.0283	374	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	77.9922	295	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_003992595.1	s__Muricauda sp002452975	77.9899	234	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_008040165.1	s__Muricauda hymeniacidonis	77.9627	413	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013090115.1	s__Muricauda amphidinii	77.8658	349	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001683915.1	s__Muricauda sp001683915	77.86	324	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.66	99.66	0.95	0.95	2	-
GCF_003584165.1	s__Muricauda sp003584165	77.8453	265	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002699205.1	s__Muricauda sp002699205	77.7904	195	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_002813125.1	s__Muricauda sp002813125	77.7808	233	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004916895.1	s__Muricauda alvinocaridis	77.752	295	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500845.1	s__Muricauda sediminis	77.5957	243	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313275.1	s__Muricauda lutimaris_A	77.3611	254	1271	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:04,844] [INFO] GTDB search result was written to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:04,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:04,848] [INFO] DFAST_QC result json was written to GCF_900129665.1_IMG-taxon_2617270824_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:41:04,848] [INFO] DFAST_QC completed!
[2024-01-24 14:41:04,848] [INFO] Total running time: 0h1m49s