[2024-01-24 11:26:54,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,321] [INFO] DQC Reference Directory: /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference
[2024-01-24 11:26:58,221] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,222] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,223] [INFO] Running command: gunzip -c /var/lib/cwl/stgc721d279-7ba6-43c3-8851-ff9f4760caa4/GCF_010119235.1_ASM1011923v1_genomic.fna.gz | prodigal -d GCF_010119235.1_ASM1011923v1_genomic.fna/cds.fna -a GCF_010119235.1_ASM1011923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:12,362] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:12,362] [INFO] Task started: HMMsearch
[2024-01-24 11:27:12,362] [INFO] Running command: hmmsearch --tblout GCF_010119235.1_ASM1011923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/reference_markers.hmm GCF_010119235.1_ASM1011923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:12,637] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:12,639] [INFO] Found 6/6 markers.
[2024-01-24 11:27:12,671] [INFO] Query marker FASTA was written to GCF_010119235.1_ASM1011923v1_genomic.fna/markers.fasta
[2024-01-24 11:27:12,672] [INFO] Task started: Blastn
[2024-01-24 11:27:12,672] [INFO] Running command: blastn -query GCF_010119235.1_ASM1011923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/reference_markers.fasta -out GCF_010119235.1_ASM1011923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:13,351] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:13,358] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:13,359] [INFO] Target genome list was writen to GCF_010119235.1_ASM1011923v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:13,368] [INFO] Task started: fastANI
[2024-01-24 11:27:13,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgc721d279-7ba6-43c3-8851-ff9f4760caa4/GCF_010119235.1_ASM1011923v1_genomic.fna.gz --refList GCF_010119235.1_ASM1011923v1_genomic.fna/target_genomes.txt --output GCF_010119235.1_ASM1011923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:24,128] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:24,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:24,130] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:24,145] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:24,145] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:24,145] [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 phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	100.0	1098	1101	95	conclusive
Flavobacterium silvisoli	strain=RD-2-33	GCA_004329815.1	2529433	2529433	type	True	81.8164	661	1101	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	79.8267	527	1101	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	78.9945	370	1101	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	78.9754	370	1101	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	78.8073	384	1101	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	78.6411	358	1101	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	78.0426	196	1101	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.9715	121	1101	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.8803	209	1101	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	77.7844	112	1101	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.7804	188	1101	95	below_threshold
Flavobacterium sufflavum	strain=BBQ-12	GCA_004016525.1	1921138	1921138	type	True	77.6877	188	1101	95	below_threshold
Flavobacterium orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	77.6606	221	1101	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.6349	184	1101	95	below_threshold
Flavobacterium pokkalii	strain=L1I52	GCA_014596575.1	1940408	1940408	type	True	77.6333	185	1101	95	below_threshold
Flavobacterium rhamnosiphilum	strain=LB3P52	GCA_004349195.1	2541724	2541724	type	True	77.6093	201	1101	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.5571	118	1101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,147] [INFO] DFAST Taxonomy check result was written to GCF_010119235.1_ASM1011923v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:24,148] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:24,148] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:24,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/checkm_data
[2024-01-24 11:27:24,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:24,183] [INFO] Task started: CheckM
[2024-01-24 11:27:24,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119235.1_ASM1011923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119235.1_ASM1011923v1_genomic.fna/checkm_input GCF_010119235.1_ASM1011923v1_genomic.fna/checkm_result
[2024-01-24 11:28:07,315] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:07,317] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:07,338] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:07,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:07,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119235.1_ASM1011923v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:07,339] [INFO] Task started: Blastn
[2024-01-24 11:28:07,340] [INFO] Running command: blastn -query GCF_010119235.1_ASM1011923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55721e7e-51ec-4965-a2fe-105772036990/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119235.1_ASM1011923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:08,353] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:08,357] [INFO] Selected 11 target genomes.
[2024-01-24 11:28:08,358] [INFO] Target genome list was writen to GCF_010119235.1_ASM1011923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:08,366] [INFO] Task started: fastANI
[2024-01-24 11:28:08,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgc721d279-7ba6-43c3-8851-ff9f4760caa4/GCF_010119235.1_ASM1011923v1_genomic.fna.gz --refList GCF_010119235.1_ASM1011923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119235.1_ASM1011923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:15,872] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:15,884] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:15,884] [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_010119235.1	s__Flavobacterium phycosphaerae	100.0	1098	1101	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_004329815.1	s__Flavobacterium silvisoli	81.8001	662	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011742145.1	s__Flavobacterium sp011742145	80.7168	529	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014486695.1	s__Flavobacterium buctense	80.6771	532	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634615.1	s__Flavobacterium sp002482945	80.6454	585	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_013072765.1	s__Flavobacterium sp013072765	80.3959	554	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004797125.1	s__Flavobacterium sangjuense	79.7646	525	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786385.1	s__Flavobacterium sp002786385	79.74	464	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	96.61	96.61	0.88	0.88	2	-
GCF_014486675.1	s__Flavobacterium macrobrachii	78.9896	371	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	-
GCA_017303755.1	s__Flavobacterium sp017303755	78.1218	344	1101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902795.1	s__Flavobacterium sp903902795	77.6355	220	1101	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 11:28:15,886] [INFO] GTDB search result was written to GCF_010119235.1_ASM1011923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:15,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:15,890] [INFO] DFAST_QC result json was written to GCF_010119235.1_ASM1011923v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:15,890] [INFO] DFAST_QC completed!
[2024-01-24 11:28:15,890] [INFO] Total running time: 0h1m22s