[2024-01-24 15:26:38,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference
[2024-01-24 15:26:39,962] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,967] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,968] [INFO] Running command: gunzip -c /var/lib/cwl/stgf69909f4-2ead-464e-b24d-2732969b1e12/GCF_002831565.1_ASM283156v1_genomic.fna.gz | prodigal -d GCF_002831565.1_ASM283156v1_genomic.fna/cds.fna -a GCF_002831565.1_ASM283156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:19,831] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:19,831] [INFO] Task started: HMMsearch
[2024-01-24 15:27:19,831] [INFO] Running command: hmmsearch --tblout GCF_002831565.1_ASM283156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/reference_markers.hmm GCF_002831565.1_ASM283156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:20,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:20,221] [INFO] Found 6/6 markers.
[2024-01-24 15:27:20,288] [INFO] Query marker FASTA was written to GCF_002831565.1_ASM283156v1_genomic.fna/markers.fasta
[2024-01-24 15:27:20,289] [INFO] Task started: Blastn
[2024-01-24 15:27:20,289] [INFO] Running command: blastn -query GCF_002831565.1_ASM283156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/reference_markers.fasta -out GCF_002831565.1_ASM283156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:20,926] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:20,930] [INFO] Selected 14 target genomes.
[2024-01-24 15:27:20,931] [INFO] Target genome list was writen to GCF_002831565.1_ASM283156v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:20,942] [INFO] Task started: fastANI
[2024-01-24 15:27:20,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69909f4-2ead-464e-b24d-2732969b1e12/GCF_002831565.1_ASM283156v1_genomic.fna.gz --refList GCF_002831565.1_ASM283156v1_genomic.fna/target_genomes.txt --output GCF_002831565.1_ASM283156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:42,254] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:42,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:42,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:42,267] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:42,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:42,267] [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
Spirosoma pollinicola	strain=Ha7	GCA_002831565.1	2057025	2057025	type	True	100.0	2931	2931	95	conclusive
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	79.603	1068	2931	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	79.475	1088	2931	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	79.095	846	2931	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	78.771	604	2931	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	78.125	573	2931	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	77.9698	802	2931	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.7878	607	2931	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	77.6693	590	2931	95	below_threshold
Spirosoma aureum	strain=BT328	GCA_011604685.1	2692134	2692134	type	True	77.6497	566	2931	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.9908	387	2931	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	76.2514	228	2931	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	76.0125	192	2931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:42,270] [INFO] DFAST Taxonomy check result was written to GCF_002831565.1_ASM283156v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:42,270] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:42,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:42,271] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/checkm_data
[2024-01-24 15:27:42,272] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:42,357] [INFO] Task started: CheckM
[2024-01-24 15:27:42,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002831565.1_ASM283156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002831565.1_ASM283156v1_genomic.fna/checkm_input GCF_002831565.1_ASM283156v1_genomic.fna/checkm_result
[2024-01-24 15:29:29,439] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:29,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:29,478] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:29,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:29,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002831565.1_ASM283156v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:29,480] [INFO] Task started: Blastn
[2024-01-24 15:29:29,480] [INFO] Running command: blastn -query GCF_002831565.1_ASM283156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a7c0038-03c0-4982-aeb6-98f59821ef5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002831565.1_ASM283156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:30,236] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:30,243] [INFO] Selected 15 target genomes.
[2024-01-24 15:29:30,244] [INFO] Target genome list was writen to GCF_002831565.1_ASM283156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:30,255] [INFO] Task started: fastANI
[2024-01-24 15:29:30,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgf69909f4-2ead-464e-b24d-2732969b1e12/GCF_002831565.1_ASM283156v1_genomic.fna.gz --refList GCF_002831565.1_ASM283156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002831565.1_ASM283156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:54,148] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:54,171] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:54,172] [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_002831565.1	s__Spirosoma pollinicola	100.0	2931	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000974425.1	s__Spirosoma radiotolerans	79.5981	1069	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000024525.1	s__Spirosoma linguale	79.5516	1113	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	79.4701	1089	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112365.1	s__Spirosoma endophyticum	79.1142	843	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965485.1	s__Spirosoma sp006965485	78.5309	846	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003259005.1	s__Spirosoma sp003259005	78.4582	820	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014117325.1	s__Spirosoma sp014117325	78.2187	805	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282275.1	s__Spirosoma utsteinense	78.1236	574	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
GCF_009754945.1	s__Spirosoma sp009754945	77.9742	801	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374085.1	s__Spirosoma spitsbergense	77.8531	617	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	77.7878	607	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	77.6619	588	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	77.6468	564	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.5213	434	2931	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:54,173] [INFO] GTDB search result was written to GCF_002831565.1_ASM283156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:54,174] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:54,178] [INFO] DFAST_QC result json was written to GCF_002831565.1_ASM283156v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:54,178] [INFO] DFAST_QC completed!
[2024-01-24 15:29:54,178] [INFO] Total running time: 0h3m16s