[2024-01-24 11:12:39,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,801] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference
[2024-01-24 11:12:41,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,289] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,289] [INFO] Running command: gunzip -c /var/lib/cwl/stg23798e09-ed74-400c-9919-b72006b5dad9/GCF_001593385.1_ASM159338v1_genomic.fna.gz | prodigal -d GCF_001593385.1_ASM159338v1_genomic.fna/cds.fna -a GCF_001593385.1_ASM159338v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:00,410] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:00,411] [INFO] Task started: HMMsearch
[2024-01-24 11:13:00,411] [INFO] Running command: hmmsearch --tblout GCF_001593385.1_ASM159338v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/reference_markers.hmm GCF_001593385.1_ASM159338v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:00,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:00,727] [INFO] Found 6/6 markers.
[2024-01-24 11:13:00,777] [INFO] Query marker FASTA was written to GCF_001593385.1_ASM159338v1_genomic.fna/markers.fasta
[2024-01-24 11:13:00,779] [INFO] Task started: Blastn
[2024-01-24 11:13:00,779] [INFO] Running command: blastn -query GCF_001593385.1_ASM159338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/reference_markers.fasta -out GCF_001593385.1_ASM159338v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:01,511] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:01,515] [INFO] Selected 16 target genomes.
[2024-01-24 11:13:01,515] [INFO] Target genome list was writen to GCF_001593385.1_ASM159338v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:01,522] [INFO] Task started: fastANI
[2024-01-24 11:13:01,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg23798e09-ed74-400c-9919-b72006b5dad9/GCF_001593385.1_ASM159338v1_genomic.fna.gz --refList GCF_001593385.1_ASM159338v1_genomic.fna/target_genomes.txt --output GCF_001593385.1_ASM159338v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:19,483] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:19,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:19,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:19,507] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:19,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:19,508] [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
Chryseobacterium cucumeris	strain=GSE06	GCA_001593385.1	1813611	1813611	type	True	100.0	1761	1761	95	conclusive
Chryseobacterium candidae	strain=JC507	GCA_004916905.1	1978493	1978493	type	True	90.022	1278	1761	95	below_threshold
Chryseobacterium gleum	strain=ATCC 35910	GCA_000143785.1	250	250	type	True	87.5509	1334	1761	95	below_threshold
Chryseobacterium gleum	strain=NCTC11432	GCA_900636535.1	250	250	type	True	87.5043	1348	1761	95	below_threshold
Chryseobacterium gleum	strain=FDAARGOS_1103	GCA_016766875.1	250	250	type	True	87.4936	1348	1761	95	below_threshold
Chryseobacterium rhizoplanae	strain=DSM 29371	GCA_900182655.1	1609531	1609531	type	True	87.353	1365	1761	95	below_threshold
Chryseobacterium sediminis	strain=IMT-174	GCA_008386505.1	1679494	1679494	type	True	87.2919	1339	1761	95	below_threshold
Chryseobacterium panacisoli	strain=Gsoil 183	GCA_008274625.1	1807141	1807141	type	True	87.2392	1336	1761	95	below_threshold
Chryseobacterium aureum	strain=17S1E7	GCA_003971235.1	2497456	2497456	type	True	86.8134	1329	1761	95	below_threshold
Chryseobacterium culicis	strain=DSM 23031	GCA_900108365.1	680127	680127	type	True	86.4665	1302	1761	95	below_threshold
Chryseobacterium viscerum	strain=687B-08	GCA_002899945.2	1037377	1037377	type	True	86.3255	1347	1761	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.6589	715	1761	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.4856	785	1761	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.0856	808	1761	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	79.8225	525	1761	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	79.3565	619	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:19,510] [INFO] DFAST Taxonomy check result was written to GCF_001593385.1_ASM159338v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:19,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:19,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:19,511] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/checkm_data
[2024-01-24 11:13:19,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:19,569] [INFO] Task started: CheckM
[2024-01-24 11:13:19,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001593385.1_ASM159338v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001593385.1_ASM159338v1_genomic.fna/checkm_input GCF_001593385.1_ASM159338v1_genomic.fna/checkm_result
[2024-01-24 11:14:17,274] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:17,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:17,297] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:17,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:17,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001593385.1_ASM159338v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:17,298] [INFO] Task started: Blastn
[2024-01-24 11:14:17,298] [INFO] Running command: blastn -query GCF_001593385.1_ASM159338v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1af796f-3c1a-4654-9b5d-4bcff872f9b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001593385.1_ASM159338v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:18,193] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:18,197] [INFO] Selected 9 target genomes.
[2024-01-24 11:14:18,197] [INFO] Target genome list was writen to GCF_001593385.1_ASM159338v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:18,204] [INFO] Task started: fastANI
[2024-01-24 11:14:18,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg23798e09-ed74-400c-9919-b72006b5dad9/GCF_001593385.1_ASM159338v1_genomic.fna.gz --refList GCF_001593385.1_ASM159338v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001593385.1_ASM159338v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:29,855] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:29,870] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:29,870] [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_001593385.1	s__Chryseobacterium cucumeris	100.0	1761	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.67	98.29	0.93	0.90	5	conclusive
GCF_016775705.1	s__Chryseobacterium sp003182335	92.5017	1391	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.03	95.49	0.90	0.89	5	-
GCF_000745535.1	s__Chryseobacterium sp000745535	92.2831	1426	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347605.1	s__Chryseobacterium sp003347605	92.161	1390	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025665.1	s__Chryseobacterium indologenes_F	91.846	1478	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799375.1	s__Chryseobacterium aquifrigidense	90.5301	1448	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.62	98.62	0.95	0.95	2	-
GCF_004119445.1	s__Chryseobacterium sp004119445	88.0712	1274	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006829085.1	s__Chryseobacterium sp006829085	86.8968	1350	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.29	97.29	0.93	0.93	2	-
GCF_003971235.1	s__Chryseobacterium aureum	86.8134	1329	1761	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:29,871] [INFO] GTDB search result was written to GCF_001593385.1_ASM159338v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:29,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:29,875] [INFO] DFAST_QC result json was written to GCF_001593385.1_ASM159338v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:29,875] [INFO] DFAST_QC completed!
[2024-01-24 11:14:29,875] [INFO] Total running time: 0h1m50s