[2024-01-24 11:51:24,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference
[2024-01-24 11:51:26,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,059] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,059] [INFO] Running command: gunzip -c /var/lib/cwl/stgc634589f-d570-4962-9db1-3c6272456ee3/GCF_004801375.1_ASM480137v1_genomic.fna.gz | prodigal -d GCF_004801375.1_ASM480137v1_genomic.fna/cds.fna -a GCF_004801375.1_ASM480137v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:41,911] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:41,911] [INFO] Task started: HMMsearch
[2024-01-24 11:51:41,911] [INFO] Running command: hmmsearch --tblout GCF_004801375.1_ASM480137v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/reference_markers.hmm GCF_004801375.1_ASM480137v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:42,174] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:42,175] [INFO] Found 6/6 markers.
[2024-01-24 11:51:42,249] [INFO] Query marker FASTA was written to GCF_004801375.1_ASM480137v1_genomic.fna/markers.fasta
[2024-01-24 11:51:42,250] [INFO] Task started: Blastn
[2024-01-24 11:51:42,250] [INFO] Running command: blastn -query GCF_004801375.1_ASM480137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/reference_markers.fasta -out GCF_004801375.1_ASM480137v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:42,994] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:42,998] [INFO] Selected 16 target genomes.
[2024-01-24 11:51:42,998] [INFO] Target genome list was writen to GCF_004801375.1_ASM480137v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:43,025] [INFO] Task started: fastANI
[2024-01-24 11:51:43,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgc634589f-d570-4962-9db1-3c6272456ee3/GCF_004801375.1_ASM480137v1_genomic.fna.gz --refList GCF_004801375.1_ASM480137v1_genomic.fna/target_genomes.txt --output GCF_004801375.1_ASM480137v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:52,532] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:52,533] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:52,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:52,547] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:52,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:52,548] [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 supellecticarium	strain=CC-CTC003	GCA_004801375.1	2565924	2565924	type	True	100.0	1274	1274	95	conclusive
Flavobacterium inviolabile	strain=P2-65	GCA_013389455.1	2748320	2748320	type	True	81.2205	729	1274	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	78.7466	328	1274	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000498475.1	510946	510946	type	True	78.7217	336	1274	95	below_threshold
Flavobacterium cauense	strain=R2A-7	GCA_000769815.1	510946	510946	type	True	78.6667	332	1274	95	below_threshold
Flavobacterium saliperosum	strain=S13	GCA_000498515.1	329186	329186	type	True	78.6077	312	1274	95	below_threshold
Flavobacterium saliperosum	strain=CGMCC 1.3801	GCA_900100625.1	329186	329186	type	True	78.602	317	1274	95	below_threshold
Flavobacterium suncheonense	strain=DSM 17707	GCA_000430025.1	350894	350894	type	True	78.4133	291	1274	95	below_threshold
Flavobacterium limnosediminis	strain=JC2902	GCA_000498535.1	1401027	1401027	type	True	78.3866	297	1274	95	below_threshold
Flavobacterium suncheonense	strain=GH29-5	GCA_000769835.1	350894	350894	type	True	78.3222	290	1274	95	below_threshold
Flavobacterium amniphilum	strain=KYPY10	GCA_023634845.1	1834035	1834035	type	True	77.7303	194	1274	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.6152	174	1274	95	below_threshold
Flavobacterium litorale	strain=WSW3-B6	GCA_019613795.1	2856519	2856519	type	True	77.3077	115	1274	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	77.1547	159	1274	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.9654	135	1274	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	76.7304	91	1274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:52,550] [INFO] DFAST Taxonomy check result was written to GCF_004801375.1_ASM480137v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:52,551] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:52,551] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:52,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/checkm_data
[2024-01-24 11:51:52,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:52,597] [INFO] Task started: CheckM
[2024-01-24 11:51:52,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004801375.1_ASM480137v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004801375.1_ASM480137v1_genomic.fna/checkm_input GCF_004801375.1_ASM480137v1_genomic.fna/checkm_result
[2024-01-24 11:52:40,110] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:40,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:40,135] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:40,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:40,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004801375.1_ASM480137v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:40,137] [INFO] Task started: Blastn
[2024-01-24 11:52:40,137] [INFO] Running command: blastn -query GCF_004801375.1_ASM480137v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b73215d-c05d-48e8-a159-639b907b1793/dqc_reference/reference_markers_gtdb.fasta -out GCF_004801375.1_ASM480137v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:41,097] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:41,101] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:41,101] [INFO] Target genome list was writen to GCF_004801375.1_ASM480137v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:41,110] [INFO] Task started: fastANI
[2024-01-24 11:52:41,110] [INFO] Running command: fastANI --query /var/lib/cwl/stgc634589f-d570-4962-9db1-3c6272456ee3/GCF_004801375.1_ASM480137v1_genomic.fna.gz --refList GCF_004801375.1_ASM480137v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004801375.1_ASM480137v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:48,727] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:48,737] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:48,738] [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_004801375.1	s__Flavobacterium sp004801375	100.0	1274	1274	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_013389455.1	s__Flavobacterium sp001898245	81.2195	731	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.49	98.42	0.93	0.92	4	-
GCF_000498475.1	s__Flavobacterium cauense	78.7217	336	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900100625.1	s__Flavobacterium saliperosum	78.6074	317	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000430025.1	s__Flavobacterium suncheonense	78.4469	291	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000498495.1	s__Flavobacterium enshiense	78.3902	280	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000498535.1	s__Flavobacterium limnosediminis	78.3866	297	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959765.1	s__Flavobacterium sp004959765	77.6589	160	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344925.1	s__Flavobacterium arcticum	77.2282	116	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013072765.1	s__Flavobacterium sp013072765	77.0819	180	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837025.1	s__Flavobacterium sp903837025	76.1744	80	1274	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 11:52:48,741] [INFO] GTDB search result was written to GCF_004801375.1_ASM480137v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:48,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:48,748] [INFO] DFAST_QC result json was written to GCF_004801375.1_ASM480137v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:48,748] [INFO] DFAST_QC completed!
[2024-01-24 11:52:48,748] [INFO] Total running time: 0h1m24s