[2024-01-24 12:14:35,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference
[2024-01-24 12:14:36,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,814] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg426bb3c1-255d-4b1e-a976-ef4adfc40a7c/GCF_004363695.1_ASM436369v1_genomic.fna.gz | prodigal -d GCF_004363695.1_ASM436369v1_genomic.fna/cds.fna -a GCF_004363695.1_ASM436369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:46,428] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:46,429] [INFO] Task started: HMMsearch
[2024-01-24 12:14:46,429] [INFO] Running command: hmmsearch --tblout GCF_004363695.1_ASM436369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/reference_markers.hmm GCF_004363695.1_ASM436369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:46,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:46,694] [INFO] Found 6/6 markers.
[2024-01-24 12:14:46,720] [INFO] Query marker FASTA was written to GCF_004363695.1_ASM436369v1_genomic.fna/markers.fasta
[2024-01-24 12:14:46,721] [INFO] Task started: Blastn
[2024-01-24 12:14:46,721] [INFO] Running command: blastn -query GCF_004363695.1_ASM436369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/reference_markers.fasta -out GCF_004363695.1_ASM436369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:47,438] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:47,440] [INFO] Selected 11 target genomes.
[2024-01-24 12:14:47,441] [INFO] Target genome list was writen to GCF_004363695.1_ASM436369v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:47,531] [INFO] Task started: fastANI
[2024-01-24 12:14:47,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg426bb3c1-255d-4b1e-a976-ef4adfc40a7c/GCF_004363695.1_ASM436369v1_genomic.fna.gz --refList GCF_004363695.1_ASM436369v1_genomic.fna/target_genomes.txt --output GCF_004363695.1_ASM436369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:54,473] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:54,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:54,474] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:54,484] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:54,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:54,485] [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 cheniae	strain=DSM 22462	GCA_004363695.1	295428	295428	type	True	100.0	905	906	95	conclusive
Flavobacterium cheniae	strain=CGMCC 1.6844	GCA_007830415.1	295428	295428	type	True	99.9629	893	906	95	conclusive
Flavobacterium aquaticum	strain=CGMCC 1.12398	GCA_003259835.1	1236486	1236486	type	True	88.9113	766	906	95	below_threshold
Flavobacterium sasangense	strain=DSM 21067	GCA_000686885.1	503361	503361	type	True	87.9451	705	906	95	below_threshold
Flavobacterium proteolyticum	strain=1Y8A	GCA_015223105.1	2911683	2911683	type	True	87.8951	733	906	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	85.2998	667	906	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	84.9817	691	906	95	below_threshold
Flavobacterium cucumis	strain=DSM 18830	GCA_900148835.1	416016	416016	type	True	84.7013	623	906	95	below_threshold
Flavobacterium celericrescens	strain=TWA-26	GCA_011392075.1	2709780	2709780	type	True	84.6542	605	906	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.4201	386	906	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	77.1342	136	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:54,487] [INFO] DFAST Taxonomy check result was written to GCF_004363695.1_ASM436369v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:54,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:54,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:54,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/checkm_data
[2024-01-24 12:14:54,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:54,524] [INFO] Task started: CheckM
[2024-01-24 12:14:54,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363695.1_ASM436369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363695.1_ASM436369v1_genomic.fna/checkm_input GCF_004363695.1_ASM436369v1_genomic.fna/checkm_result
[2024-01-24 12:15:26,100] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:26,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,124] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:26,124] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:26,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363695.1_ASM436369v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:26,125] [INFO] Task started: Blastn
[2024-01-24 12:15:26,125] [INFO] Running command: blastn -query GCF_004363695.1_ASM436369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8e0e401-f81c-43cc-8b56-f1c3dcfa666f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363695.1_ASM436369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,180] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,184] [INFO] Selected 9 target genomes.
[2024-01-24 12:15:27,185] [INFO] Target genome list was writen to GCF_004363695.1_ASM436369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:27,192] [INFO] Task started: fastANI
[2024-01-24 12:15:27,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg426bb3c1-255d-4b1e-a976-ef4adfc40a7c/GCF_004363695.1_ASM436369v1_genomic.fna.gz --refList GCF_004363695.1_ASM436369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363695.1_ASM436369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:33,441] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:33,450] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:33,450] [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_004363695.1	s__Flavobacterium cheniae	100.0	905	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_003497625.1	s__Flavobacterium sp003497625	92.6188	728	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002483315.1	s__Flavobacterium sp002483315	92.3615	742	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009495755.1	s__Flavobacterium sp009495755	89.4863	690	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259835.1	s__Flavobacterium aquaticum	88.9113	766	906	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	87.9337	706	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223105.1	s__Flavobacterium aquaticum_A	87.8951	733	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293165.1	s__Flavobacterium sp004293165	87.007	639	906	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.30	97.30	0.81	0.81	2	-
GCA_002422095.1	s__Flavobacterium sp002422095	86.6255	544	906	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 12:15:33,452] [INFO] GTDB search result was written to GCF_004363695.1_ASM436369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:33,453] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:33,456] [INFO] DFAST_QC result json was written to GCF_004363695.1_ASM436369v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:33,456] [INFO] DFAST_QC completed!
[2024-01-24 12:15:33,456] [INFO] Total running time: 0h0m58s