[2024-01-24 15:27:19,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:19,866] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:19,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference
[2024-01-24 15:27:21,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:21,152] [INFO] Task started: Prodigal
[2024-01-24 15:27:21,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg715c9e01-4b2d-4532-90d3-ca9e1b31388f/GCF_900446785.1_52700_H01_genomic.fna.gz | prodigal -d GCF_900446785.1_52700_H01_genomic.fna/cds.fna -a GCF_900446785.1_52700_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:37,732] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:37,732] [INFO] Task started: HMMsearch
[2024-01-24 15:27:37,732] [INFO] Running command: hmmsearch --tblout GCF_900446785.1_52700_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/reference_markers.hmm GCF_900446785.1_52700_H01_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:38,027] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:38,029] [INFO] Found 6/6 markers.
[2024-01-24 15:27:38,076] [INFO] Query marker FASTA was written to GCF_900446785.1_52700_H01_genomic.fna/markers.fasta
[2024-01-24 15:27:38,077] [INFO] Task started: Blastn
[2024-01-24 15:27:38,077] [INFO] Running command: blastn -query GCF_900446785.1_52700_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/reference_markers.fasta -out GCF_900446785.1_52700_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:38,777] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:38,782] [INFO] Selected 11 target genomes.
[2024-01-24 15:27:38,783] [INFO] Target genome list was writen to GCF_900446785.1_52700_H01_genomic.fna/target_genomes.txt
[2024-01-24 15:27:38,787] [INFO] Task started: fastANI
[2024-01-24 15:27:38,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg715c9e01-4b2d-4532-90d3-ca9e1b31388f/GCF_900446785.1_52700_H01_genomic.fna.gz --refList GCF_900446785.1_52700_H01_genomic.fna/target_genomes.txt --output GCF_900446785.1_52700_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:50,155] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:50,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:50,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:50,172] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:50,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:50,172] [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 balustinum	strain=NCTC11212	GCA_900446785.1	246	246	type	True	100.0	1499	1504	95	conclusive
Chryseobacterium balustinum	strain=DSM 16775	GCA_900168205.1	246	246	type	True	99.9416	1431	1504	95	conclusive
Chryseobacterium piscium	strain=CCUG 51923	GCA_003385415.1	333702	333702	type	True	94.0879	1042	1504	95	below_threshold
Chryseobacterium mulctrae	strain=CA10	GCA_006175945.1	2576777	2576777	type	True	90.3896	1119	1504	95	below_threshold
Chryseobacterium scophthalmum	strain=DSM 16779	GCA_900143185.1	59733	59733	type	True	90.3504	1114	1504	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	90.2643	1085	1504	95	below_threshold
Chryseobacterium indoltheticum	strain=ATCC 27950	GCA_900156145.1	254	254	type	True	89.4592	1031	1504	95	below_threshold
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	81.4247	801	1504	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	80.8895	627	1504	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_020985365.1	2852098	2852098	type	True	77.5208	181	1504	95	below_threshold
Chryseobacterium faecale	strain=F4	GCA_019195395.1	2852098	2852098	type	True	77.5021	182	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:50,174] [INFO] DFAST Taxonomy check result was written to GCF_900446785.1_52700_H01_genomic.fna/tc_result.tsv
[2024-01-24 15:27:50,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:50,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:50,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/checkm_data
[2024-01-24 15:27:50,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:50,219] [INFO] Task started: CheckM
[2024-01-24 15:27:50,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900446785.1_52700_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900446785.1_52700_H01_genomic.fna/checkm_input GCF_900446785.1_52700_H01_genomic.fna/checkm_result
[2024-01-24 15:28:38,641] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:38,643] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:38,662] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:38,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:38,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900446785.1_52700_H01_genomic.fna/markers.fasta)
[2024-01-24 15:28:38,663] [INFO] Task started: Blastn
[2024-01-24 15:28:38,664] [INFO] Running command: blastn -query GCF_900446785.1_52700_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2040b02-5860-4302-91b3-5ce82719ae60/dqc_reference/reference_markers_gtdb.fasta -out GCF_900446785.1_52700_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:39,534] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:39,537] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:39,537] [INFO] Target genome list was writen to GCF_900446785.1_52700_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:39,544] [INFO] Task started: fastANI
[2024-01-24 15:28:39,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg715c9e01-4b2d-4532-90d3-ca9e1b31388f/GCF_900446785.1_52700_H01_genomic.fna.gz --refList GCF_900446785.1_52700_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900446785.1_52700_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:47,697] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:47,703] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:47,703] [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_900168205.1	s__Chryseobacterium balustinum	99.9269	1434	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.96	99.93	0.98	0.95	3	conclusive
GCF_003385415.1	s__Chryseobacterium piscium	94.1067	1041	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.69	96.60	0.88	0.87	3	-
GCF_001677955.1	s__Chryseobacterium sp001677955	91.9147	1149	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006175945.1	s__Chryseobacterium mulctrae	90.3715	1118	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143185.1	s__Chryseobacterium scophthalmum	90.3594	1113	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.42	95.16	0.86	0.85	5	-
GCF_903166575.1	s__Chryseobacterium sp903166575	90.2643	1085	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779605.1	s__Chryseobacterium sp014779605	89.8126	1124	1504	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.70	96.70	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:47,705] [INFO] GTDB search result was written to GCF_900446785.1_52700_H01_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:47,705] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:47,708] [INFO] DFAST_QC result json was written to GCF_900446785.1_52700_H01_genomic.fna/dqc_result.json
[2024-01-24 15:28:47,708] [INFO] DFAST_QC completed!
[2024-01-24 15:28:47,708] [INFO] Total running time: 0h1m28s