[2024-01-24 12:48:04,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:04,946] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:04,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference
[2024-01-24 12:48:06,171] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:06,172] [INFO] Task started: Prodigal
[2024-01-24 12:48:06,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg743db550-5c8d-4d06-9bb3-e48abf1162b3/GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/cds.fna -a GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:24,081] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:24,081] [INFO] Task started: HMMsearch
[2024-01-24 12:48:24,081] [INFO] Running command: hmmsearch --tblout GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/reference_markers.hmm GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:24,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:24,423] [INFO] Found 6/6 markers.
[2024-01-24 12:48:24,471] [INFO] Query marker FASTA was written to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:48:24,472] [INFO] Task started: Blastn
[2024-01-24 12:48:24,472] [INFO] Running command: blastn -query GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/reference_markers.fasta -out GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:25,216] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:25,221] [INFO] Selected 15 target genomes.
[2024-01-24 12:48:25,221] [INFO] Target genome list was writen to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:48:25,227] [INFO] Task started: fastANI
[2024-01-24 12:48:25,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg743db550-5c8d-4d06-9bb3-e48abf1162b3/GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna.gz --refList GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:39,457] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:39,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:39,459] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:39,481] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:39,481] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:39,481] [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 arachidis	strain=DSM 27619	GCA_900129245.1	1416778	1416778	type	True	100.0	1625	1628	95	conclusive
Chryseobacterium ginsenosidimutans	strain=THG 15	GCA_024807225.1	687846	687846	type	True	83.1169	1030	1628	95	below_threshold
Chryseobacterium wanjuense	strain=DSM 17724	GCA_900111495.1	356305	356305	type	True	82.8527	963	1628	95	below_threshold
Chryseobacterium mucoviscidosis	strain=VT16-26	GCA_002177115.1	1945581	1945581	type	True	82.8356	907	1628	95	below_threshold
Chryseobacterium gambrini	strain=DSM 18014	GCA_900156825.1	373672	373672	type	True	82.7864	921	1628	95	below_threshold
Chryseobacterium geocarposphaerae	strain=DSM 27617	GCA_002797535.1	1416776	1416776	type	True	82.7346	874	1628	95	below_threshold
Chryseobacterium gwangjuense	strain=THG-A18	GCA_021311115.1	1069980	1069980	type	True	82.3784	794	1628	95	below_threshold
Chryseobacterium tagetis	strain=RG1	GCA_016735585.2	2801334	2801334	type	True	82.363	872	1628	95	below_threshold
Chryseobacterium daeguense	strain=DSM 19388	GCA_000430825.1	412438	412438	type	True	82.1104	859	1628	95	below_threshold
Chryseobacterium formosense	strain=DSM 17452	GCA_900116415.1	236814	236814	type	True	81.4467	815	1628	95	below_threshold
Chryseobacterium cheonjiense	strain=RJ-7-14	GCA_012927265.1	2728845	2728845	type	True	80.8616	825	1628	95	below_threshold
Chryseobacterium schmidteae	strain=Marseille-P9602	GCA_903166575.1	2730404	2730404	type	True	80.4622	754	1628	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_002943655.1	297244	297244	type	True	80.0606	703	1628	95	below_threshold
Chryseobacterium shigense	strain=DSM 17126	GCA_900156575.1	297244	297244	type	True	80.036	702	1628	95	below_threshold
Chryseobacterium fistulae	strain=CECT 9393	GCA_902729325.1	2675058	2675058	type	True	78.8778	500	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:39,483] [INFO] DFAST Taxonomy check result was written to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:48:39,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:39,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:39,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/checkm_data
[2024-01-24 12:48:39,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:39,535] [INFO] Task started: CheckM
[2024-01-24 12:48:39,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/checkm_input GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:49:34,059] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:34,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:34,088] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:34,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:34,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:49:34,089] [INFO] Task started: Blastn
[2024-01-24 12:49:34,090] [INFO] Running command: blastn -query GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg03782e08-ba18-4716-95c2-b59d50fca896/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:34,988] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:34,991] [INFO] Selected 15 target genomes.
[2024-01-24 12:49:34,991] [INFO] Target genome list was writen to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:35,037] [INFO] Task started: fastANI
[2024-01-24 12:49:35,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg743db550-5c8d-4d06-9bb3-e48abf1162b3/GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna.gz --refList GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:49,266] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:49,291] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:49,292] [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_900129245.1	s__Chryseobacterium arachidis	100.0	1625	1628	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_000799195.1	s__Chryseobacterium sp000799195	83.3638	1007	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455915.1	s__Chryseobacterium sp002455915	83.2179	769	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425355.1	s__Chryseobacterium sp001425355	82.9452	998	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111495.1	s__Chryseobacterium wanjuense	82.8667	962	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002177115.1	s__Chryseobacterium mucoviscidosis	82.831	907	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.26	95.97	0.86	0.75	7	-
GCF_900156825.1	s__Chryseobacterium gambrini	82.7716	923	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.1494	96.49	96.36	0.87	0.82	3	-
GCF_002797535.1	s__Chryseobacterium geocarposphaerae	82.7157	876	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	95.65	95.65	0.87	0.87	2	-
GCF_018603435.1	s__Chryseobacterium sp013153155	82.6719	913	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	96.28	96.28	0.93	0.93	2	-
GCF_000813825.1	s__Chryseobacterium taiwanense	82.631	885	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156075.1	s__Chryseobacterium sp900156075	82.6305	696	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799455.1	s__Chryseobacterium sp000799455	82.5815	903	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799515.1	s__Chryseobacterium sp000799515	81.5015	737	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116415.1	s__Chryseobacterium formosense	81.4638	813	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	98.74	97.50	0.90	0.80	3	-
GCF_900156575.1	s__Chryseobacterium shigense	80.0237	704	1628	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Weeksellaceae;g__Chryseobacterium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:49,293] [INFO] GTDB search result was written to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:49,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:49,298] [INFO] DFAST_QC result json was written to GCF_900129245.1_IMG-taxon_2695420930_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:49:49,298] [INFO] DFAST_QC completed!
[2024-01-24 12:49:49,298] [INFO] Total running time: 0h1m44s