[2024-01-24 11:43:25,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,079] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,079] [INFO] DQC Reference Directory: /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference
[2024-01-24 11:43:30,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,058] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg05291aa5-df54-481b-9721-c8de1f3d9b27/GCF_014638005.1_ASM1463800v1_genomic.fna.gz | prodigal -d GCF_014638005.1_ASM1463800v1_genomic.fna/cds.fna -a GCF_014638005.1_ASM1463800v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:43,006] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:43,006] [INFO] Task started: HMMsearch
[2024-01-24 11:43:43,006] [INFO] Running command: hmmsearch --tblout GCF_014638005.1_ASM1463800v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/reference_markers.hmm GCF_014638005.1_ASM1463800v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:43,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:43,263] [INFO] Found 6/6 markers.
[2024-01-24 11:43:43,290] [INFO] Query marker FASTA was written to GCF_014638005.1_ASM1463800v1_genomic.fna/markers.fasta
[2024-01-24 11:43:43,291] [INFO] Task started: Blastn
[2024-01-24 11:43:43,291] [INFO] Running command: blastn -query GCF_014638005.1_ASM1463800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/reference_markers.fasta -out GCF_014638005.1_ASM1463800v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:44,010] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:44,014] [INFO] Selected 17 target genomes.
[2024-01-24 11:43:44,015] [INFO] Target genome list was writen to GCF_014638005.1_ASM1463800v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:44,023] [INFO] Task started: fastANI
[2024-01-24 11:43:44,023] [INFO] Running command: fastANI --query /var/lib/cwl/stg05291aa5-df54-481b-9721-c8de1f3d9b27/GCF_014638005.1_ASM1463800v1_genomic.fna.gz --refList GCF_014638005.1_ASM1463800v1_genomic.fna/target_genomes.txt --output GCF_014638005.1_ASM1463800v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:54,430] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:54,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:54,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:54,445] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:43:54,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:54,446] [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 orientale	strain=CGMCC 1.12506	GCA_014638005.1	1756020	1756020	type	True	100.0	1067	1071	95	conclusive
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	81.954	582	1071	95	below_threshold
Flavobacterium piscinae	strain=ICH-30	GCA_004122145.1	2506424	2506424	type	True	80.953	511	1071	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	80.7073	506	1071	95	below_threshold
Flavobacterium macrobrachii	strain=LMG 25203	GCA_014385475.2	591204	591204	type	True	77.9102	276	1071	95	below_threshold
Flavobacterium macrobrachii	strain=an-8	GCA_014486675.1	591204	591204	type	True	77.892	276	1071	95	below_threshold
Flavobacterium solisilvae	strain=SE-s27	GCA_012911605.1	1852019	1852019	type	True	77.8274	291	1071	95	below_threshold
Flavobacterium dankookense	strain=DSM 25687	GCA_004362665.1	706186	706186	type	True	77.7699	277	1071	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	77.721	262	1071	95	below_threshold
Flavobacterium phycosphaerae	strain=MK012	GCA_010119235.1	2697515	2697515	type	True	77.6293	231	1071	95	below_threshold
Flavobacterium amnicola	strain=LLJ-11	GCA_004122165.1	2506422	2506422	type	True	77.6283	215	1071	95	below_threshold
Flavobacterium cyclinae	strain=KSM-R2A25	GCA_021172145.1	2895947	2895947	type	True	77.5744	273	1071	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	77.4669	156	1071	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	77.362	189	1071	95	below_threshold
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	77.207	224	1071	95	below_threshold
Flavobacterium jumunjinense	strain=HME7102	GCA_021650975.2	998845	998845	type	True	77.0505	213	1071	95	below_threshold
Flavobacterium branchiophilum	strain=DSM 24789	GCA_006716585.1	55197	55197	type	True	76.9627	144	1071	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:54,454] [INFO] DFAST Taxonomy check result was written to GCF_014638005.1_ASM1463800v1_genomic.fna/tc_result.tsv
[2024-01-24 11:43:54,455] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:54,455] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:54,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/checkm_data
[2024-01-24 11:43:54,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:54,499] [INFO] Task started: CheckM
[2024-01-24 11:43:54,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638005.1_ASM1463800v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638005.1_ASM1463800v1_genomic.fna/checkm_input GCF_014638005.1_ASM1463800v1_genomic.fna/checkm_result
[2024-01-24 11:44:35,652] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:35,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,672] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:35,672] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:35,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638005.1_ASM1463800v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:35,673] [INFO] Task started: Blastn
[2024-01-24 11:44:35,673] [INFO] Running command: blastn -query GCF_014638005.1_ASM1463800v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf407f1bf-8844-4155-bc0f-5fd98d77225b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638005.1_ASM1463800v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,634] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,638] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:36,639] [INFO] Target genome list was writen to GCF_014638005.1_ASM1463800v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:36,645] [INFO] Task started: fastANI
[2024-01-24 11:44:36,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg05291aa5-df54-481b-9721-c8de1f3d9b27/GCF_014638005.1_ASM1463800v1_genomic.fna.gz --refList GCF_014638005.1_ASM1463800v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638005.1_ASM1463800v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:42,217] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:42,232] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:42,233] [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_014638005.1	s__Flavobacterium orientale	100.0	1067	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002428305.1	s__Flavobacterium sp002428305	91.2858	793	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352205.1	s__Flavobacterium sp002352205	83.4735	588	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.95	99.95	0.86	0.86	2	-
GCF_003268815.1	s__Flavobacterium lacus	81.9663	581	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004122145.1	s__Flavobacterium piscinae	80.9538	510	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.76	99.76	1.00	1.00	2	-
GCF_000425465.1	s__Flavobacterium filum	80.7076	506	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302935.1	s__Flavobacterium sp017302935	80.5264	434	1071	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822155.1	s__Flavobacterium sp013822155	80.2195	450	1071	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 11:44:42,235] [INFO] GTDB search result was written to GCF_014638005.1_ASM1463800v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:42,236] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:42,241] [INFO] DFAST_QC result json was written to GCF_014638005.1_ASM1463800v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:42,242] [INFO] DFAST_QC completed!
[2024-01-24 11:44:42,242] [INFO] Total running time: 0h1m17s