[2024-01-24 12:14:49,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference
[2024-01-24 12:14:50,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,360] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,360] [INFO] Running command: gunzip -c /var/lib/cwl/stgb28ebd97-8663-4e0c-9a8b-e384b673d7ce/GCF_002217405.1_ASM221740v1_genomic.fna.gz | prodigal -d GCF_002217405.1_ASM221740v1_genomic.fna/cds.fna -a GCF_002217405.1_ASM221740v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:59,370] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:59,371] [INFO] Task started: HMMsearch
[2024-01-24 12:14:59,371] [INFO] Running command: hmmsearch --tblout GCF_002217405.1_ASM221740v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/reference_markers.hmm GCF_002217405.1_ASM221740v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:59,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:59,619] [INFO] Found 6/6 markers.
[2024-01-24 12:14:59,649] [INFO] Query marker FASTA was written to GCF_002217405.1_ASM221740v1_genomic.fna/markers.fasta
[2024-01-24 12:14:59,649] [INFO] Task started: Blastn
[2024-01-24 12:14:59,649] [INFO] Running command: blastn -query GCF_002217405.1_ASM221740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/reference_markers.fasta -out GCF_002217405.1_ASM221740v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:00,343] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:00,347] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:00,347] [INFO] Target genome list was writen to GCF_002217405.1_ASM221740v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:00,354] [INFO] Task started: fastANI
[2024-01-24 12:15:00,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ebd97-8663-4e0c-9a8b-e384b673d7ce/GCF_002217405.1_ASM221740v1_genomic.fna.gz --refList GCF_002217405.1_ASM221740v1_genomic.fna/target_genomes.txt --output GCF_002217405.1_ASM221740v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:11,079] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:11,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:11,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:11,096] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:15:11,096] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:11,097] [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 psychrophilum	strain=ATCC 49418	GCA_002217405.1	96345	96345	type	True	100.0	832	837	95	conclusive
Flavobacterium psychrophilum	strain=FPG3	GCA_000754405.1	96345	96345	type	True	99.9829	837	837	95	conclusive
Flavobacterium psychrophilum	strain=DSM 3660	GCA_900101925.1	96345	96345	type	True	99.9639	827	837	95	conclusive
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	85.6414	618	837	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	78.0954	239	837	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	77.9726	239	837	95	below_threshold
Flavobacterium geliluteum	strain=P7388	GCA_017948595.1	2816120	2816120	type	True	77.8832	234	837	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	77.8645	199	837	95	below_threshold
Flavobacterium hibernum	strain=ATCC 51468	GCA_002217315.1	37752	37752	type	True	77.8061	256	837	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.602	239	837	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.5778	210	837	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	77.5447	239	837	95	below_threshold
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	77.3084	164	837	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.1168	62	837	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.6892	101	837	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:11,100] [INFO] DFAST Taxonomy check result was written to GCF_002217405.1_ASM221740v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:11,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:11,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:11,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/checkm_data
[2024-01-24 12:15:11,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:11,133] [INFO] Task started: CheckM
[2024-01-24 12:15:11,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002217405.1_ASM221740v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002217405.1_ASM221740v1_genomic.fna/checkm_input GCF_002217405.1_ASM221740v1_genomic.fna/checkm_result
[2024-01-24 12:15:41,584] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:41,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,611] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:41,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:41,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002217405.1_ASM221740v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:41,612] [INFO] Task started: Blastn
[2024-01-24 12:15:41,612] [INFO] Running command: blastn -query GCF_002217405.1_ASM221740v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5062bb2d-a698-4e22-82a4-9c9d03a61c26/dqc_reference/reference_markers_gtdb.fasta -out GCF_002217405.1_ASM221740v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:42,549] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:42,553] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:42,553] [INFO] Target genome list was writen to GCF_002217405.1_ASM221740v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:42,567] [INFO] Task started: fastANI
[2024-01-24 12:15:42,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgb28ebd97-8663-4e0c-9a8b-e384b673d7ce/GCF_002217405.1_ASM221740v1_genomic.fna.gz --refList GCF_002217405.1_ASM221740v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002217405.1_ASM221740v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:55,996] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:56,026] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:56,027] [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_002217405.1	s__Flavobacterium psychrophilum	100.0	832	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.22	98.91	0.92	0.83	157	conclusive
GCF_900111965.1	s__Flavobacterium swingsii	85.6405	618	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097365.1	s__Flavobacterium franklandianum	78.5773	227	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.99	98.99	0.94	0.94	2	-
GCF_003634825.1	s__Flavobacterium sp003634825	78.3351	224	837	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	78.3016	246	837	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	78.1744	209	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027725.1	s__Flavobacterium sp001027725	78.1537	186	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097385.1	s__Flavobacterium sp007097385	78.1085	244	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097265.1	s__Flavobacterium gawalongense	78.0954	239	837	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	77.991	222	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	77.9481	240	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832125.1	s__Flavobacterium hibernum	77.9118	247	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.99	0.99	3	-
GCA_003449615.1	s__Flavobacterium sp003449615	77.8723	157	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948595.1	s__Flavobacterium sp017948595	77.8658	234	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902804475.1	s__Flavobacterium bizetiae	77.7102	235	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.96	99.94	0.99	0.99	3	-
GCF_012911605.1	s__Flavobacterium sp012911605	77.5708	237	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842575.1	s__Flavobacterium sp903842575	77.5158	193	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917885.1	s__Flavobacterium croceum	77.4083	191	837	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	77.3207	173	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352205.1	s__Flavobacterium sp002352205	77.2187	165	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCA_903819815.1	s__Flavobacterium sp903819815	77.1447	162	837	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,030] [INFO] GTDB search result was written to GCF_002217405.1_ASM221740v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:56,031] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:56,037] [INFO] DFAST_QC result json was written to GCF_002217405.1_ASM221740v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:56,038] [INFO] DFAST_QC completed!
[2024-01-24 12:15:56,038] [INFO] Total running time: 0h1m7s