[2024-01-25 18:52:35,673] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:35,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:35,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference
[2024-01-25 18:52:36,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:36,784] [INFO] Task started: Prodigal
[2024-01-25 18:52:36,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ab383de-4377-4060-a906-b8d0dde81fd2/GCF_014385475.1_ASM1438547v2_genomic.fna.gz | prodigal -d GCF_014385475.1_ASM1438547v2_genomic.fna/cds.fna -a GCF_014385475.1_ASM1438547v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:46,980] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:46,981] [INFO] Task started: HMMsearch
[2024-01-25 18:52:46,981] [INFO] Running command: hmmsearch --tblout GCF_014385475.1_ASM1438547v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/reference_markers.hmm GCF_014385475.1_ASM1438547v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:47,185] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:47,186] [INFO] Found 6/6 markers.
[2024-01-25 18:52:47,211] [INFO] Query marker FASTA was written to GCF_014385475.1_ASM1438547v2_genomic.fna/markers.fasta
[2024-01-25 18:52:47,211] [INFO] Task started: Blastn
[2024-01-25 18:52:47,212] [INFO] Running command: blastn -query GCF_014385475.1_ASM1438547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/reference_markers.fasta -out GCF_014385475.1_ASM1438547v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:47,839] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:47,842] [INFO] Selected 12 target genomes.
[2024-01-25 18:52:47,842] [INFO] Target genome list was writen to GCF_014385475.1_ASM1438547v2_genomic.fna/target_genomes.txt
[2024-01-25 18:52:47,847] [INFO] Task started: fastANI
[2024-01-25 18:52:47,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab383de-4377-4060-a906-b8d0dde81fd2/GCF_014385475.1_ASM1438547v2_genomic.fna.gz --refList GCF_014385475.1_ASM1438547v2_genomic.fna/target_genomes.txt --output GCF_014385475.1_ASM1438547v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:56,387] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:56,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:56,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:56,395] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:56,395] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:56,396] [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 macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	100.0	1030	1040	95	conclusive
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	99.9815	984	1040	95	conclusive
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	91.0127	725	1040	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	87.1246	704	1040	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	80.4409	477	1040	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	80.0534	469	1040	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	79.2081	423	1040	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.5341	308	1040	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.2992	244	1040	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.2582	171	1040	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.1995	165	1040	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	76.9997	229	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:56,397] [INFO] DFAST Taxonomy check result was written to GCF_014385475.1_ASM1438547v2_genomic.fna/tc_result.tsv
[2024-01-25 18:52:56,397] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:56,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:56,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/checkm_data
[2024-01-25 18:52:56,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:56,433] [INFO] Task started: CheckM
[2024-01-25 18:52:56,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385475.1_ASM1438547v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385475.1_ASM1438547v2_genomic.fna/checkm_input GCF_014385475.1_ASM1438547v2_genomic.fna/checkm_result
[2024-01-25 18:53:29,496] [INFO] Task succeeded: CheckM
[2024-01-25 18:53:29,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:53:29,514] [INFO] ===== Completeness check finished =====
[2024-01-25 18:53:29,514] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:53:29,515] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385475.1_ASM1438547v2_genomic.fna/markers.fasta)
[2024-01-25 18:53:29,515] [INFO] Task started: Blastn
[2024-01-25 18:53:29,515] [INFO] Running command: blastn -query GCF_014385475.1_ASM1438547v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg456e5c70-ffa8-4942-b132-8ee56f587451/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385475.1_ASM1438547v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:30,514] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:30,516] [INFO] Selected 12 target genomes.
[2024-01-25 18:53:30,516] [INFO] Target genome list was writen to GCF_014385475.1_ASM1438547v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:53:30,530] [INFO] Task started: fastANI
[2024-01-25 18:53:30,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ab383de-4377-4060-a906-b8d0dde81fd2/GCF_014385475.1_ASM1438547v2_genomic.fna.gz --refList GCF_014385475.1_ASM1438547v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014385475.1_ASM1438547v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:53:38,606] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:38,614] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:53:38,614] [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_014486675.1	s__Flavobacterium macrobrachii	99.9815	984	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.85	97.73	0.92	0.87	3	conclusive
GCF_012911605.1	s__Flavobacterium sp012911605	91.0127	725	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362665.1	s__Flavobacterium dankookense	87.1426	703	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000757385.1	s__Flavobacterium aquatile	80.4337	476	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCA_001464475.1	s__Flavobacterium sp001464475	80.2195	480	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642275.1	s__Flavobacterium lutivivi	80.0654	468	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298525.1	s__Flavobacterium sp013298525	79.9537	405	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303755.1	s__Flavobacterium sp017303755	79.688	390	1040	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	79.3319	465	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_004797125.1	s__Flavobacterium sangjuense	79.2068	422	1040	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014486695.1	s__Flavobacterium buctense	79.1813	423	1040	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	77.9271	318	1040	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 18:53:38,616] [INFO] GTDB search result was written to GCF_014385475.1_ASM1438547v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:53:38,616] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:53:38,619] [INFO] DFAST_QC result json was written to GCF_014385475.1_ASM1438547v2_genomic.fna/dqc_result.json
[2024-01-25 18:53:38,619] [INFO] DFAST_QC completed!
[2024-01-25 18:53:38,619] [INFO] Total running time: 0h1m3s