[2024-01-25 20:18:50,476] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:18:50,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:18:50,478] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference
[2024-01-25 20:18:51,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:18:51,647] [INFO] Task started: Prodigal
[2024-01-25 20:18:51,647] [INFO] Running command: gunzip -c /var/lib/cwl/stge764d13e-f558-4c37-9e36-c44e688e6a2c/GCF_014486675.1_ASM1448667v1_genomic.fna.gz | prodigal -d GCF_014486675.1_ASM1448667v1_genomic.fna/cds.fna -a GCF_014486675.1_ASM1448667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:01,836] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:01,836] [INFO] Task started: HMMsearch
[2024-01-25 20:19:01,836] [INFO] Running command: hmmsearch --tblout GCF_014486675.1_ASM1448667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/reference_markers.hmm GCF_014486675.1_ASM1448667v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:02,054] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:02,055] [INFO] Found 6/6 markers.
[2024-01-25 20:19:02,083] [INFO] Query marker FASTA was written to GCF_014486675.1_ASM1448667v1_genomic.fna/markers.fasta
[2024-01-25 20:19:02,084] [INFO] Task started: Blastn
[2024-01-25 20:19:02,084] [INFO] Running command: blastn -query GCF_014486675.1_ASM1448667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/reference_markers.fasta -out GCF_014486675.1_ASM1448667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:02,743] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:02,746] [INFO] Selected 12 target genomes.
[2024-01-25 20:19:02,746] [INFO] Target genome list was writen to GCF_014486675.1_ASM1448667v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:02,751] [INFO] Task started: fastANI
[2024-01-25 20:19:02,751] [INFO] Running command: fastANI --query /var/lib/cwl/stge764d13e-f558-4c37-9e36-c44e688e6a2c/GCF_014486675.1_ASM1448667v1_genomic.fna.gz --refList GCF_014486675.1_ASM1448667v1_genomic.fna/target_genomes.txt --output GCF_014486675.1_ASM1448667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:11,006] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:11,007] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:11,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:11,016] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:19:11,016] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:11,016] [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=an-8	GCA_014486675.1	591204	591204	type	True	100.0	1045	1054	95	conclusive
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	99.9812	1028	1054	95	conclusive
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	90.8702	729	1054	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	87.2718	691	1054	95	below_threshold
Flavobacterium aquatile	strain=LMG 4008	GCA_000757385.1	245	245	type	True	80.3962	478	1054	95	below_threshold
Flavobacterium lutivivi	strain=CGMCC 1.15347	GCA_014642275.1	1677894	1677894	type	True	80.174	454	1054	95	below_threshold
Flavobacterium sangjuense	strain=GS03	GCA_004797125.1	2518177	2518177	type	True	79.2126	420	1054	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	78.6812	304	1054	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.4426	167	1054	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.4104	240	1054	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.0909	172	1054	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.0567	223	1054	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:11,017] [INFO] DFAST Taxonomy check result was written to GCF_014486675.1_ASM1448667v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:11,018] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:11,019] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:11,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/checkm_data
[2024-01-25 20:19:11,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:11,056] [INFO] Task started: CheckM
[2024-01-25 20:19:11,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014486675.1_ASM1448667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014486675.1_ASM1448667v1_genomic.fna/checkm_input GCF_014486675.1_ASM1448667v1_genomic.fna/checkm_result
[2024-01-25 20:19:43,759] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:43,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:43,776] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:43,776] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:43,776] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014486675.1_ASM1448667v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:43,777] [INFO] Task started: Blastn
[2024-01-25 20:19:43,777] [INFO] Running command: blastn -query GCF_014486675.1_ASM1448667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0906d9-73c8-4eb0-bb43-4018933262f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_014486675.1_ASM1448667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:44,717] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:44,721] [INFO] Selected 12 target genomes.
[2024-01-25 20:19:44,721] [INFO] Target genome list was writen to GCF_014486675.1_ASM1448667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:44,754] [INFO] Task started: fastANI
[2024-01-25 20:19:44,754] [INFO] Running command: fastANI --query /var/lib/cwl/stge764d13e-f558-4c37-9e36-c44e688e6a2c/GCF_014486675.1_ASM1448667v1_genomic.fna.gz --refList GCF_014486675.1_ASM1448667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014486675.1_ASM1448667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:52,685] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:52,693] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:19:52,693] [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	100.0	1045	1054	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	90.8702	729	1054	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	87.2848	691	1054	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	80.4005	479	1054	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	80.3811	478	1054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_014642275.1	s__Flavobacterium lutivivi	80.1541	456	1054	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	80.0862	407	1054	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	79.7679	394	1054	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	79.319	476	1054	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.37	98.37	0.85	0.85	2	-
GCF_014486695.1	s__Flavobacterium buctense	79.2126	412	1054	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	79.1793	423	1054	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	77.9369	320	1054	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 20:19:52,695] [INFO] GTDB search result was written to GCF_014486675.1_ASM1448667v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:52,695] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:52,698] [INFO] DFAST_QC result json was written to GCF_014486675.1_ASM1448667v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:52,699] [INFO] DFAST_QC completed!
[2024-01-25 20:19:52,699] [INFO] Total running time: 0h1m2s