[2024-01-25 17:38:05,511] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:05,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:05,517] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference
[2024-01-25 17:38:06,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:06,660] [INFO] Task started: Prodigal
[2024-01-25 17:38:06,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg73f51649-b2bf-4e09-9e3a-a95cd87fbc74/GCF_013389455.1_ASM1338945v1_genomic.fna.gz | prodigal -d GCF_013389455.1_ASM1338945v1_genomic.fna/cds.fna -a GCF_013389455.1_ASM1338945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:19,787] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:19,788] [INFO] Task started: HMMsearch
[2024-01-25 17:38:19,788] [INFO] Running command: hmmsearch --tblout GCF_013389455.1_ASM1338945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/reference_markers.hmm GCF_013389455.1_ASM1338945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:20,096] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:20,097] [INFO] Found 6/6 markers.
[2024-01-25 17:38:20,132] [INFO] Query marker FASTA was written to GCF_013389455.1_ASM1338945v1_genomic.fna/markers.fasta
[2024-01-25 17:38:20,132] [INFO] Task started: Blastn
[2024-01-25 17:38:20,132] [INFO] Running command: blastn -query GCF_013389455.1_ASM1338945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/reference_markers.fasta -out GCF_013389455.1_ASM1338945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:20,810] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:20,812] [INFO] Selected 16 target genomes.
[2024-01-25 17:38:20,813] [INFO] Target genome list was writen to GCF_013389455.1_ASM1338945v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:20,817] [INFO] Task started: fastANI
[2024-01-25 17:38:20,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f51649-b2bf-4e09-9e3a-a95cd87fbc74/GCF_013389455.1_ASM1338945v1_genomic.fna.gz --refList GCF_013389455.1_ASM1338945v1_genomic.fna/target_genomes.txt --output GCF_013389455.1_ASM1338945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:30,759] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:30,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:30,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:30,769] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:30,769] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:30,770] [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 inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	100.0	1301	1304	95	conclusive
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	81.3135	704	1304	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	78.7255	330	1304	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	78.6818	351	1304	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	78.67	348	1304	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	78.6655	343	1304	95	below_threshold
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	78.6593	331	1304	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	78.6067	327	1304	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	78.5591	166	1304	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	78.5244	303	1304	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	78.4348	305	1304	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	78.4132	86	1304	95	below_threshold
Flavobacterium panacis	strain=DCY106	GCA_024649945.1	2962567	2962567	type	True	77.725	185	1304	95	below_threshold
Flavobacterium columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	77.5514	104	1304	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.7686	54	1304	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:30,774] [INFO] DFAST Taxonomy check result was written to GCF_013389455.1_ASM1338945v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:30,775] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:30,775] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:30,775] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/checkm_data
[2024-01-25 17:38:30,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:30,819] [INFO] Task started: CheckM
[2024-01-25 17:38:30,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013389455.1_ASM1338945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013389455.1_ASM1338945v1_genomic.fna/checkm_input GCF_013389455.1_ASM1338945v1_genomic.fna/checkm_result
[2024-01-25 17:39:10,155] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:10,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:10,175] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:10,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:10,175] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013389455.1_ASM1338945v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:10,175] [INFO] Task started: Blastn
[2024-01-25 17:39:10,175] [INFO] Running command: blastn -query GCF_013389455.1_ASM1338945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb3070ba-1e7a-49c9-91ff-f67b3d18f4e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013389455.1_ASM1338945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:11,191] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:11,195] [INFO] Selected 13 target genomes.
[2024-01-25 17:39:11,196] [INFO] Target genome list was writen to GCF_013389455.1_ASM1338945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:11,203] [INFO] Task started: fastANI
[2024-01-25 17:39:11,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg73f51649-b2bf-4e09-9e3a-a95cd87fbc74/GCF_013389455.1_ASM1338945v1_genomic.fna.gz --refList GCF_013389455.1_ASM1338945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013389455.1_ASM1338945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:20,798] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:20,807] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:20,807] [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_013389455.1	s__Flavobacterium sp001898245	100.0	1302	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	conclusive
GCF_004801375.1	s__Flavobacterium sp004801375	81.3037	705	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498475.1	s__Flavobacterium cauense	78.6818	347	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_000498535.1	s__Flavobacterium limnosediminis	78.6597	330	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100625.1	s__Flavobacterium saliperosum	78.5945	328	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000498495.1	s__Flavobacterium enshiense	78.5184	301	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000430025.1	s__Flavobacterium suncheonense	78.4863	287	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002217245.1	s__Flavobacterium columnare_A	77.9435	100	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_900148835.1	s__Flavobacterium cucumis	77.8901	145	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003865365.1	s__Flavobacterium macacae	77.6995	185	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002530675.1	s__Flavobacterium columnare	77.5396	107	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	-
GCF_004349195.1	s__Flavobacterium sp004349195	77.4353	154	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007109225.1	s__Flavobacterium sp007109225	77.3545	196	1304	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:20,809] [INFO] GTDB search result was written to GCF_013389455.1_ASM1338945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:20,809] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:20,813] [INFO] DFAST_QC result json was written to GCF_013389455.1_ASM1338945v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:20,813] [INFO] DFAST_QC completed!
[2024-01-25 17:39:20,813] [INFO] Total running time: 0h1m15s