[2024-01-24 12:45:09,829] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference
[2024-01-24 12:45:13,084] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,085] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,086] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7a9adde-8572-40ac-8a1e-e86cb2b45fd2/GCF_007990835.1_ASM799083v1_genomic.fna.gz | prodigal -d GCF_007990835.1_ASM799083v1_genomic.fna/cds.fna -a GCF_007990835.1_ASM799083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:21,410] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:21,411] [INFO] Task started: HMMsearch
[2024-01-24 12:45:21,411] [INFO] Running command: hmmsearch --tblout GCF_007990835.1_ASM799083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/reference_markers.hmm GCF_007990835.1_ASM799083v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:21,672] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:21,673] [INFO] Found 6/6 markers.
[2024-01-24 12:45:21,704] [INFO] Query marker FASTA was written to GCF_007990835.1_ASM799083v1_genomic.fna/markers.fasta
[2024-01-24 12:45:21,705] [INFO] Task started: Blastn
[2024-01-24 12:45:21,705] [INFO] Running command: blastn -query GCF_007990835.1_ASM799083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/reference_markers.fasta -out GCF_007990835.1_ASM799083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:22,362] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:22,366] [INFO] Selected 14 target genomes.
[2024-01-24 12:45:22,366] [INFO] Target genome list was writen to GCF_007990835.1_ASM799083v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:22,405] [INFO] Task started: fastANI
[2024-01-24 12:45:22,405] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7a9adde-8572-40ac-8a1e-e86cb2b45fd2/GCF_007990835.1_ASM799083v1_genomic.fna.gz --refList GCF_007990835.1_ASM799083v1_genomic.fna/target_genomes.txt --output GCF_007990835.1_ASM799083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:30,772] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:30,773] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:30,773] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:30,786] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:45:30,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:30,786] [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 columnare	strain=NBRC 100251	GCA_007990835.1	996	996	type	True	100.0	912	924	95	conclusive
Flavobacterium columnare	strain=ATCC 23463	GCA_002530675.1	996	996	type	True	99.9533	888	924	95	conclusive
Flavobacterium davisii	strain=90-106	GCA_019565505.1	2906077	2906077	type	True	84.9837	792	924	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	83.9511	751	924	95	below_threshold
Flavobacterium terrae	strain=DSM 18829	GCA_900142035.1	415425	415425	type	True	78.4695	290	924	95	below_threshold
Flavobacterium supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	78.2065	86	924	95	below_threshold
Flavobacterium haoranii	strain=DSM 22807	GCA_900142055.1	683124	683124	type	True	77.8842	189	924	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.7476	197	924	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	77.6337	162	924	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	77.5609	178	924	95	below_threshold
Flavobacterium alkalisoli	strain=XS-5	GCA_008000935.1	2602769	2602769	type	True	77.2444	66	924	95	below_threshold
Flavobacterium granuli	strain=DSM 17797	GCA_003003155.1	280093	280093	type	True	77.2357	98	924	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	76.7721	137	924	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3903	70	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:30,788] [INFO] DFAST Taxonomy check result was written to GCF_007990835.1_ASM799083v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:30,789] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:30,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:30,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/checkm_data
[2024-01-24 12:45:30,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:30,827] [INFO] Task started: CheckM
[2024-01-24 12:45:30,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007990835.1_ASM799083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007990835.1_ASM799083v1_genomic.fna/checkm_input GCF_007990835.1_ASM799083v1_genomic.fna/checkm_result
[2024-01-24 12:46:01,048] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:01,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:01,073] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:01,074] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:01,075] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007990835.1_ASM799083v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:01,076] [INFO] Task started: Blastn
[2024-01-24 12:46:01,076] [INFO] Running command: blastn -query GCF_007990835.1_ASM799083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg421d7980-67f9-434c-809a-757c8e888aaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_007990835.1_ASM799083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:02,102] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:02,107] [INFO] Selected 9 target genomes.
[2024-01-24 12:46:02,107] [INFO] Target genome list was writen to GCF_007990835.1_ASM799083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:02,124] [INFO] Task started: fastANI
[2024-01-24 12:46:02,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7a9adde-8572-40ac-8a1e-e86cb2b45fd2/GCF_007990835.1_ASM799083v1_genomic.fna.gz --refList GCF_007990835.1_ASM799083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007990835.1_ASM799083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:07,777] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:07,792] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:07,792] [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_002530675.1	s__Flavobacterium columnare	99.9533	888	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.33	99.02	0.96	0.93	39	conclusive
GCA_002217245.1	s__Flavobacterium columnare_A	91.3917	775	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.08	98.79	0.92	0.89	11	-
GCF_900290975.1	s__Flavobacterium columnare_D	85.0343	751	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.86	98.55	0.90	0.88	3	-
GCF_002204895.1	s__Flavobacterium columnare_C	83.9595	740	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.67	99.21	0.94	0.90	7	-
GCF_004959765.1	s__Flavobacterium sp004959765	78.583	278	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142035.1	s__Flavobacterium terrae	78.4838	289	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801375.1	s__Flavobacterium sp004801375	78.1638	87	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686885.1	s__Flavobacterium sasangense	77.5609	178	924	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464475.1	s__Flavobacterium sp001464475	77.4812	164	924	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 12:46:07,793] [INFO] GTDB search result was written to GCF_007990835.1_ASM799083v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:07,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:07,797] [INFO] DFAST_QC result json was written to GCF_007990835.1_ASM799083v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:07,797] [INFO] DFAST_QC completed!
[2024-01-24 12:46:07,797] [INFO] Total running time: 0h0m58s