[2024-01-24 15:27:41,312] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:41,314] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:41,314] [INFO] DQC Reference Directory: /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference
[2024-01-24 15:27:43,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:43,883] [INFO] Task started: Prodigal
[2024-01-24 15:27:43,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg265aac63-2307-4bdd-b357-bc79f37c8dd5/GCF_004349085.1_ASM434908v1_genomic.fna.gz | prodigal -d GCF_004349085.1_ASM434908v1_genomic.fna/cds.fna -a GCF_004349085.1_ASM434908v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:58,667] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:58,667] [INFO] Task started: HMMsearch
[2024-01-24 15:27:58,667] [INFO] Running command: hmmsearch --tblout GCF_004349085.1_ASM434908v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/reference_markers.hmm GCF_004349085.1_ASM434908v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:58,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:58,935] [INFO] Found 6/6 markers.
[2024-01-24 15:27:58,968] [INFO] Query marker FASTA was written to GCF_004349085.1_ASM434908v1_genomic.fna/markers.fasta
[2024-01-24 15:27:58,969] [INFO] Task started: Blastn
[2024-01-24 15:27:58,969] [INFO] Running command: blastn -query GCF_004349085.1_ASM434908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/reference_markers.fasta -out GCF_004349085.1_ASM434908v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:59,648] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:59,651] [INFO] Selected 18 target genomes.
[2024-01-24 15:27:59,651] [INFO] Target genome list was writen to GCF_004349085.1_ASM434908v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:59,659] [INFO] Task started: fastANI
[2024-01-24 15:27:59,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg265aac63-2307-4bdd-b357-bc79f37c8dd5/GCF_004349085.1_ASM434908v1_genomic.fna.gz --refList GCF_004349085.1_ASM434908v1_genomic.fna/target_genomes.txt --output GCF_004349085.1_ASM434908v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:13,920] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:13,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:13,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:13,937] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:13,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:13,938] [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 caseinilyticum	strain=AT-3-2	GCA_004349085.1	2541732	2541732	type	True	100.0	1261	1263	95	conclusive
Flavobacterium psychrolimnae	strain=LMG 22018	GCA_003312425.1	249351	249351	type	True	87.6645	876	1263	95	below_threshold
Flavobacterium petrolei	strain=Kopri-42	GCA_003314435.2	2259594	2259594	type	True	87.1945	828	1263	95	below_threshold
Flavobacterium limicola	strain=DSM 15094	GCA_003634755.1	180441	180441	type	True	86.6248	764	1263	95	below_threshold
Flavobacterium sinopsychrotolerans	strain=CGMCC 1.8704	GCA_900110375.1	604089	604089	type	True	86.5865	796	1263	95	below_threshold
Flavobacterium xueshanense	strain=CGMCC 1.9227	GCA_900112975.1	935223	935223	type	True	86.2117	801	1263	95	below_threshold
Flavobacterium glaciei	strain=DSM 19728	GCA_003350545.1	386300	386300	type	True	85.309	756	1263	95	below_threshold
Flavobacterium glaciei	strain=CGMCC 1.5380	GCA_007994155.1	386300	386300	type	True	85.2565	760	1263	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	84.8826	754	1263	95	below_threshold
Flavobacterium ranwuense	strain=LB2P22	GCA_004349315.1	2541725	2541725	type	True	84.5878	794	1263	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	82.5821	699	1263	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	82.3185	696	1263	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	82.1425	707	1263	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.552	370	1263	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	78.4792	370	1263	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.3123	349	1263	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.295	344	1263	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	76.5584	74	1263	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:13,939] [INFO] DFAST Taxonomy check result was written to GCF_004349085.1_ASM434908v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:13,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:13,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:13,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/checkm_data
[2024-01-24 15:28:13,941] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:13,983] [INFO] Task started: CheckM
[2024-01-24 15:28:13,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349085.1_ASM434908v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349085.1_ASM434908v1_genomic.fna/checkm_input GCF_004349085.1_ASM434908v1_genomic.fna/checkm_result
[2024-01-24 15:28:59,057] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:59,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:59,077] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:59,077] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:59,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349085.1_ASM434908v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:59,079] [INFO] Task started: Blastn
[2024-01-24 15:28:59,079] [INFO] Running command: blastn -query GCF_004349085.1_ASM434908v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg018c7733-4e17-4437-beb6-fd94eceb917f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349085.1_ASM434908v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:00,021] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:00,025] [INFO] Selected 15 target genomes.
[2024-01-24 15:29:00,025] [INFO] Target genome list was writen to GCF_004349085.1_ASM434908v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:00,038] [INFO] Task started: fastANI
[2024-01-24 15:29:00,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg265aac63-2307-4bdd-b357-bc79f37c8dd5/GCF_004349085.1_ASM434908v1_genomic.fna.gz --refList GCF_004349085.1_ASM434908v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349085.1_ASM434908v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:12,350] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:12,376] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:12,376] [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_004349085.1	s__Flavobacterium caseinilyticum	100.0	1261	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003312425.1	s__Flavobacterium psychrolimnae	87.702	873	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752255.1	s__Flavobacterium sp015752255	87.6363	877	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003314435.2	s__Flavobacterium petrolei	87.1873	830	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.35	97.35	0.87	0.87	2	-
GCF_003634755.1	s__Flavobacterium limicola	86.6404	763	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110375.1	s__Flavobacterium sinopsychrotolerans	86.5839	796	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112975.1	s__Flavobacterium xueshanense	86.2117	801	1263	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	85.6875	851	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.44	97.44	0.88	0.88	2	-
GCF_003350545.1	s__Flavobacterium glaciei	85.3202	755	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004349195.1	s__Flavobacterium sp004349195	84.882	754	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349315.1	s__Flavobacterium sp004349315	84.6105	792	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.48	98.48	0.90	0.90	2	-
GCF_900108015.1	s__Flavobacterium urumqiense	82.3185	696	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744835.1	s__Flavobacterium sp000744835	82.2852	665	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142885.1	s__Flavobacterium xinjiangense	82.1501	706	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875765.1	s__Flavobacterium sp017875765	81.5191	667	1263	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.17	98.17	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:12,383] [INFO] GTDB search result was written to GCF_004349085.1_ASM434908v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:12,383] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:12,388] [INFO] DFAST_QC result json was written to GCF_004349085.1_ASM434908v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:12,388] [INFO] DFAST_QC completed!
[2024-01-24 15:29:12,388] [INFO] Total running time: 0h1m31s