[2024-01-24 13:02:03,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,920] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference
[2024-01-24 13:02:05,186] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,187] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,187] [INFO] Running command: gunzip -c /var/lib/cwl/stg644b8da9-6988-49eb-b94c-14bfd10d30ee/GCF_003545715.1_ASM354571v1_genomic.fna.gz | prodigal -d GCF_003545715.1_ASM354571v1_genomic.fna/cds.fna -a GCF_003545715.1_ASM354571v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:35,023] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:35,023] [INFO] Task started: HMMsearch
[2024-01-24 13:02:35,024] [INFO] Running command: hmmsearch --tblout GCF_003545715.1_ASM354571v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/reference_markers.hmm GCF_003545715.1_ASM354571v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:35,287] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:35,288] [INFO] Found 6/6 markers.
[2024-01-24 13:02:35,334] [INFO] Query marker FASTA was written to GCF_003545715.1_ASM354571v1_genomic.fna/markers.fasta
[2024-01-24 13:02:35,334] [INFO] Task started: Blastn
[2024-01-24 13:02:35,335] [INFO] Running command: blastn -query GCF_003545715.1_ASM354571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/reference_markers.fasta -out GCF_003545715.1_ASM354571v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:35,907] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:35,912] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:35,912] [INFO] Target genome list was writen to GCF_003545715.1_ASM354571v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:35,920] [INFO] Task started: fastANI
[2024-01-24 13:02:35,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg644b8da9-6988-49eb-b94c-14bfd10d30ee/GCF_003545715.1_ASM354571v1_genomic.fna.gz --refList GCF_003545715.1_ASM354571v1_genomic.fna/target_genomes.txt --output GCF_003545715.1_ASM354571v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:53,887] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:53,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:53,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:53,896] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:53,896] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:53,896] [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
Taibaiella koreensis	strain=THG-DT86	GCA_003545715.1	1268548	1268548	type	True	100.0	1967	1969	95	conclusive
Taibaiella helva	strain=F-4	GCA_003545695.1	2301235	2301235	type	True	81.2688	1082	1969	95	below_threshold
Taibaiella chishuiensis	strain=CGMCC 1.12700	GCA_003014535.1	1434707	1434707	type	True	77.5225	373	1969	95	below_threshold
Taibaiella lutea	strain=KVB11	GCA_008629695.1	2608001	2608001	type	True	77.2464	128	1969	95	below_threshold
Niastella koreensis	strain=GR20-10	GCA_000246855.1	354356	354356	type	True	77.1545	51	1969	95	below_threshold
Edaphocola flava	strain=HME-24	GCA_004118155.1	2499629	2499629	type	True	76.3495	66	1969	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	76.3105	60	1969	95	below_threshold
Edaphocola aurantiacus	strain=H2	GCA_019797745.1	2601682	2601682	type	True	76.1746	70	1969	95	below_threshold
Chitinophaga lutea	strain=ZY74	GCA_003813775.1	2488634	2488634	type	True	76.0682	63	1969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:53,898] [INFO] DFAST Taxonomy check result was written to GCF_003545715.1_ASM354571v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:53,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:53,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:53,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/checkm_data
[2024-01-24 13:02:53,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:53,955] [INFO] Task started: CheckM
[2024-01-24 13:02:53,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003545715.1_ASM354571v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003545715.1_ASM354571v1_genomic.fna/checkm_input GCF_003545715.1_ASM354571v1_genomic.fna/checkm_result
[2024-01-24 13:04:12,130] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:12,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:12,152] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:12,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:12,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003545715.1_ASM354571v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:12,153] [INFO] Task started: Blastn
[2024-01-24 13:04:12,153] [INFO] Running command: blastn -query GCF_003545715.1_ASM354571v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03ae228c-2bd1-425a-b627-eb0fc42e68a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003545715.1_ASM354571v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:12,918] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:12,921] [INFO] Selected 19 target genomes.
[2024-01-24 13:04:12,922] [INFO] Target genome list was writen to GCF_003545715.1_ASM354571v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:13,000] [INFO] Task started: fastANI
[2024-01-24 13:04:13,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg644b8da9-6988-49eb-b94c-14bfd10d30ee/GCF_003545715.1_ASM354571v1_genomic.fna.gz --refList GCF_003545715.1_ASM354571v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003545715.1_ASM354571v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:28,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:28,041] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:28,041] [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_003545715.1	s__Edaphocola koreensis	100.0	1967	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003545695.1	s__Edaphocola helva	81.265	1083	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014535.1	s__Edaphocola chishuiensis	77.5254	374	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629695.1	s__Edaphocola lutea	77.2601	124	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246855.1	s__Niastella koreensis	76.937	50	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Niastella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001897155.1	s__Edaphocola sp001897155	76.8272	79	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086345.1	s__Chitinophaga sp008086345	76.8013	51	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786525.1	s__UBA1312 sp016786525	76.1781	68	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__UBA1312	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813775.1	s__Chitinophaga lutea	76.0953	62	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267915.1	s__Flavipsychrobacter sp018267915	76.0407	54	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavipsychrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897525.1	s__Edaphocola sp001897525	76.0376	80	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016786705.1	s__Edaphocola sp016786705	75.9273	71	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Edaphocola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019091455.1	s__Chitinophaga sp019091455	75.8497	69	1969	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:28,042] [INFO] GTDB search result was written to GCF_003545715.1_ASM354571v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:28,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:28,046] [INFO] DFAST_QC result json was written to GCF_003545715.1_ASM354571v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:28,046] [INFO] DFAST_QC completed!
[2024-01-24 13:04:28,046] [INFO] Total running time: 0h2m24s