[2023-06-08 06:51:24,051] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:51:24,054] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:51:24,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference
[2023-06-08 06:51:25,634] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:51:25,635] [INFO] Task started: Prodigal
[2023-06-08 06:51:25,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg5226bffc-3308-476d-a18b-031268333bbd/GCA_945897545.1_MsE-30apr19-1_genomic.fna.gz | prodigal -d GCA_945897545.1_MsE-30apr19-1_genomic.fna/cds.fna -a GCA_945897545.1_MsE-30apr19-1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:51:35,989] [INFO] Task succeeded: Prodigal
[2023-06-08 06:51:35,989] [INFO] Task started: HMMsearch
[2023-06-08 06:51:35,990] [INFO] Running command: hmmsearch --tblout GCA_945897545.1_MsE-30apr19-1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/reference_markers.hmm GCA_945897545.1_MsE-30apr19-1_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:51:36,277] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:51:36,279] [INFO] Found 6/6 markers.
[2023-06-08 06:51:36,310] [INFO] Query marker FASTA was written to GCA_945897545.1_MsE-30apr19-1_genomic.fna/markers.fasta
[2023-06-08 06:51:36,310] [INFO] Task started: Blastn
[2023-06-08 06:51:36,310] [INFO] Running command: blastn -query GCA_945897545.1_MsE-30apr19-1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/reference_markers.fasta -out GCA_945897545.1_MsE-30apr19-1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:51:37,034] [INFO] Task succeeded: Blastn
[2023-06-08 06:51:37,038] [INFO] Selected 21 target genomes.
[2023-06-08 06:51:37,039] [INFO] Target genome list was writen to GCA_945897545.1_MsE-30apr19-1_genomic.fna/target_genomes.txt
[2023-06-08 06:51:37,044] [INFO] Task started: fastANI
[2023-06-08 06:51:37,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg5226bffc-3308-476d-a18b-031268333bbd/GCA_945897545.1_MsE-30apr19-1_genomic.fna.gz --refList GCA_945897545.1_MsE-30apr19-1_genomic.fna/target_genomes.txt --output GCA_945897545.1_MsE-30apr19-1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:51:52,594] [INFO] Task succeeded: fastANI
[2023-06-08 06:51:52,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:51:52,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:51:52,611] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 06:51:52,611] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 06:51:52,612] [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
Flavobacterium franklandianum	strain=LB3P56	GCA_007097365.1	2594430	2594430	type	True	81.6874	503	816	95	below_threshold
Flavobacterium fluvii	strain=DSM 19978	GCA_900129545.1	468056	468056	type	True	80.7181	460	816	95	below_threshold
Flavobacterium nackdongense	strain=GS13	GCA_004355225.1	2547394	2547394	type	True	80.3237	469	816	95	below_threshold
Flavobacterium alvei	strain=HR-AY	GCA_002920895.1	2080416	2080416	type	True	80.3171	448	816	95	below_threshold
Flavobacterium cellulosilyticum	strain=AR-3-4	GCA_004349355.1	2541731	2541731	type	True	79.4106	425	816	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	78.7274	352	816	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	78.6921	286	816	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	78.6858	327	816	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	78.6532	285	816	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	78.6483	288	816	95	below_threshold
Flavobacterium sandaracinum	strain=LB-D12	GCA_004349135.1	2541733	2541733	type	True	78.4255	296	816	95	below_threshold
Flavobacterium psychrotolerans	strain=RB1R5	GCA_003097635.1	2169410	2169410	type	True	78.3948	256	816	95	below_threshold
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	78.3771	310	816	95	below_threshold
Flavobacterium xanthum	strain=DSM 3661	GCA_900142695.1	69322	69322	type	True	78.2634	277	816	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.1397	283	816	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	77.9659	260	816	95	below_threshold
Flavobacterium aquariorum	strain=IMCC34762	GCA_003254745.1	2217670	2217670	type	True	77.8972	259	816	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.1989	212	816	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	76.5147	120	816	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	76.3867	76	816	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 06:51:52,616] [INFO] DFAST Taxonomy check result was written to GCA_945897545.1_MsE-30apr19-1_genomic.fna/tc_result.tsv
[2023-06-08 06:51:52,617] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:51:52,617] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:51:52,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/checkm_data
[2023-06-08 06:51:52,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:51:52,653] [INFO] Task started: CheckM
[2023-06-08 06:51:52,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897545.1_MsE-30apr19-1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897545.1_MsE-30apr19-1_genomic.fna/checkm_input GCA_945897545.1_MsE-30apr19-1_genomic.fna/checkm_result
[2023-06-08 06:52:27,350] [INFO] Task succeeded: CheckM
[2023-06-08 06:52:27,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:52:27,372] [INFO] ===== Completeness check finished =====
[2023-06-08 06:52:27,372] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:52:27,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897545.1_MsE-30apr19-1_genomic.fna/markers.fasta)
[2023-06-08 06:52:27,373] [INFO] Task started: Blastn
[2023-06-08 06:52:27,373] [INFO] Running command: blastn -query GCA_945897545.1_MsE-30apr19-1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc067acf0-a39a-4074-ad30-3631b1947398/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897545.1_MsE-30apr19-1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:52:28,415] [INFO] Task succeeded: Blastn
[2023-06-08 06:52:28,420] [INFO] Selected 16 target genomes.
[2023-06-08 06:52:28,420] [INFO] Target genome list was writen to GCA_945897545.1_MsE-30apr19-1_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:52:28,423] [INFO] Task started: fastANI
[2023-06-08 06:52:28,424] [INFO] Running command: fastANI --query /var/lib/cwl/stg5226bffc-3308-476d-a18b-031268333bbd/GCA_945897545.1_MsE-30apr19-1_genomic.fna.gz --refList GCA_945897545.1_MsE-30apr19-1_genomic.fna/target_genomes_gtdb.txt --output GCA_945897545.1_MsE-30apr19-1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:52:39,346] [INFO] Task succeeded: fastANI
[2023-06-08 06:52:39,365] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 06:52:39,365] [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_007097365.1	s__Flavobacterium franklandianum	81.6875	503	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCA_014379405.1	s__Flavobacterium sp014379405	81.2035	406	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015277675.1	s__Flavobacterium soyangense	81.1936	483	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010365135.1	s__Flavobacterium sp010365135	80.8494	421	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823965.1	s__Flavobacterium sp013823965	80.7637	424	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002920895.1	s__Flavobacterium alvei	80.3244	446	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004355225.1	s__Flavobacterium nackdongense	80.2997	471	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413745.1	s__Flavobacterium sp002413745	80.2054	446	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.93	99.87	0.97	0.94	6	-
GCA_003449615.1	s__Flavobacterium sp003449615	80.0599	321	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861155.1	s__Flavobacterium sp903861155	79.9615	374	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.81	99.81	0.91	0.91	2	-
GCA_012837155.1	s__Flavobacterium sp012837155	79.7619	357	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349355.1	s__Flavobacterium cellulosilyticum	79.3852	428	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	79.3752	276	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754315.1	s__Flavobacterium sp002754315	79.0656	310	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_007097265.1	s__Flavobacterium gawalongense	78.728	352	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.69	99.40	0.97	0.94	5	-
GCF_003097635.1	s__Flavobacterium psychrotolerans	78.3795	257	816	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 06:52:39,367] [INFO] GTDB search result was written to GCA_945897545.1_MsE-30apr19-1_genomic.fna/result_gtdb.tsv
[2023-06-08 06:52:39,368] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:52:39,375] [INFO] DFAST_QC result json was written to GCA_945897545.1_MsE-30apr19-1_genomic.fna/dqc_result.json
[2023-06-08 06:52:39,375] [INFO] DFAST_QC completed!
[2023-06-08 06:52:39,376] [INFO] Total running time: 0h1m15s