[2024-01-24 10:47:40,957] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference
[2024-01-24 10:47:44,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,787] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,788] [INFO] Running command: gunzip -c /var/lib/cwl/stg20ffe461-e4d3-456b-a0c9-066ce7b855e7/GCF_016745235.1_ASM1674523v1_genomic.fna.gz | prodigal -d GCF_016745235.1_ASM1674523v1_genomic.fna/cds.fna -a GCF_016745235.1_ASM1674523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:03,093] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:03,093] [INFO] Task started: HMMsearch
[2024-01-24 10:48:03,093] [INFO] Running command: hmmsearch --tblout GCF_016745235.1_ASM1674523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/reference_markers.hmm GCF_016745235.1_ASM1674523v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:03,397] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:03,399] [INFO] Found 6/6 markers.
[2024-01-24 10:48:03,441] [INFO] Query marker FASTA was written to GCF_016745235.1_ASM1674523v1_genomic.fna/markers.fasta
[2024-01-24 10:48:03,442] [INFO] Task started: Blastn
[2024-01-24 10:48:03,442] [INFO] Running command: blastn -query GCF_016745235.1_ASM1674523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/reference_markers.fasta -out GCF_016745235.1_ASM1674523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:04,090] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:04,094] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:04,095] [INFO] Target genome list was writen to GCF_016745235.1_ASM1674523v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:04,102] [INFO] Task started: fastANI
[2024-01-24 10:48:04,102] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ffe461-e4d3-456b-a0c9-066ce7b855e7/GCF_016745235.1_ASM1674523v1_genomic.fna.gz --refList GCF_016745235.1_ASM1674523v1_genomic.fna/target_genomes.txt --output GCF_016745235.1_ASM1674523v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:19,333] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:19,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:19,334] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:19,346] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:19,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:19,346] [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 endalhagicum	strain=L7	GCA_016745235.1	2797638	2797638	type	True	100.0	1639	1639	95	conclusive
Chryseobacterium kwangjuense	strain=KJ1R5	GCA_001563495.1	267125	267125	type	True	86.0187	1300	1639	95	below_threshold
Chryseobacterium phocaeense	strain=6021061333	GCA_900169075.1	1816690	1816690	type	True	85.8645	1287	1639	95	below_threshold
Chryseobacterium oleae	strain=DSM 25575	GCA_900115055.1	491207	491207	type	True	85.6085	1284	1639	95	below_threshold
Chryseobacterium elymi	strain=KCTC 22547	GCA_003385495.1	395936	395936	type	True	84.8008	1091	1639	95	below_threshold
Chryseobacterium lathyri	strain=NBRC 105250	GCA_007991435.1	395933	395933	type	True	84.6058	1124	1639	95	below_threshold
Chryseobacterium lathyri	strain=KCTC 22544	GCA_003290185.1	395933	395933	type	True	84.5872	1131	1639	95	below_threshold
Chryseobacterium angstadtii	strain=KM	GCA_001045465.1	558151	558151	type	True	84.4065	1233	1639	95	below_threshold
Chryseobacterium oranimense	strain=DSM 19055	GCA_900129755.1	421058	421058	type	True	84.2635	1093	1639	95	below_threshold
Chryseobacterium luteum	strain=DSM 18605	GCA_000737785.1	421531	421531	type	True	84.23	1035	1639	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.3613	652	1639	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	80.3374	751	1639	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	80.1742	694	1639	95	below_threshold
Kaistella palustris	strain=DSM 21579	GCA_000422265.1	493376	493376	type	True	76.6335	114	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:19,348] [INFO] DFAST Taxonomy check result was written to GCF_016745235.1_ASM1674523v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:19,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:19,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:19,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/checkm_data
[2024-01-24 10:48:19,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:19,397] [INFO] Task started: CheckM
[2024-01-24 10:48:19,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016745235.1_ASM1674523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016745235.1_ASM1674523v1_genomic.fna/checkm_input GCF_016745235.1_ASM1674523v1_genomic.fna/checkm_result
[2024-01-24 10:49:14,209] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:14,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:14,237] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:14,237] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:14,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016745235.1_ASM1674523v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:14,238] [INFO] Task started: Blastn
[2024-01-24 10:49:14,238] [INFO] Running command: blastn -query GCF_016745235.1_ASM1674523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12e78427-0a12-4ddc-af33-e9fc116072ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_016745235.1_ASM1674523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:15,160] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:15,165] [INFO] Selected 11 target genomes.
[2024-01-24 10:49:15,165] [INFO] Target genome list was writen to GCF_016745235.1_ASM1674523v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:15,174] [INFO] Task started: fastANI
[2024-01-24 10:49:15,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ffe461-e4d3-456b-a0c9-066ce7b855e7/GCF_016745235.1_ASM1674523v1_genomic.fna.gz --refList GCF_016745235.1_ASM1674523v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016745235.1_ASM1674523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:28,843] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:28,855] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:28,855] [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_016745235.1	s__Chryseobacterium sp016745235	100.0	1639	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001563495.1	s__Chryseobacterium kwangjuense	86.0333	1298	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169075.1	s__Chryseobacterium phocaeense	85.8699	1286	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737715.1	s__Chryseobacterium sp000737715	85.6353	1264	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115055.1	s__Chryseobacterium oleae	85.6001	1285	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128945.1	s__Chryseobacterium sp900128945	85.5357	1305	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.14	97.03	0.94	0.94	3	-
GCF_003290185.1	s__Chryseobacterium lathyri	84.5961	1130	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001045465.1	s__Chryseobacterium angstadtii	84.4189	1231	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129755.1	s__Chryseobacterium oranimense	84.2599	1093	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	97.88	97.88	0.91	0.91	3	-
GCF_000737785.1	s__Chryseobacterium luteum	84.2409	1034	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207845.1	s__Chryseobacterium shigense_A	84.1566	1049	1639	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:28,857] [INFO] GTDB search result was written to GCF_016745235.1_ASM1674523v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:28,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:28,860] [INFO] DFAST_QC result json was written to GCF_016745235.1_ASM1674523v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:28,861] [INFO] DFAST_QC completed!
[2024-01-24 10:49:28,861] [INFO] Total running time: 0h1m48s