[2024-01-24 11:21:07,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,425] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference
[2024-01-24 11:21:11,960] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,961] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,961] [INFO] Running command: gunzip -c /var/lib/cwl/stgc161c6c7-aa74-4bdc-84b8-34ca2cb2dbb1/GCF_001202045.1_ASM120204v1_genomic.fna.gz | prodigal -d GCF_001202045.1_ASM120204v1_genomic.fna/cds.fna -a GCF_001202045.1_ASM120204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:23,675] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:23,675] [INFO] Task started: HMMsearch
[2024-01-24 11:21:23,676] [INFO] Running command: hmmsearch --tblout GCF_001202045.1_ASM120204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/reference_markers.hmm GCF_001202045.1_ASM120204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:23,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:23,924] [INFO] Found 6/6 markers.
[2024-01-24 11:21:23,957] [INFO] Query marker FASTA was written to GCF_001202045.1_ASM120204v1_genomic.fna/markers.fasta
[2024-01-24 11:21:23,957] [INFO] Task started: Blastn
[2024-01-24 11:21:23,958] [INFO] Running command: blastn -query GCF_001202045.1_ASM120204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/reference_markers.fasta -out GCF_001202045.1_ASM120204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:24,730] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:24,733] [INFO] Selected 13 target genomes.
[2024-01-24 11:21:24,734] [INFO] Target genome list was writen to GCF_001202045.1_ASM120204v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:24,758] [INFO] Task started: fastANI
[2024-01-24 11:21:24,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgc161c6c7-aa74-4bdc-84b8-34ca2cb2dbb1/GCF_001202045.1_ASM120204v1_genomic.fna.gz --refList GCF_001202045.1_ASM120204v1_genomic.fna/target_genomes.txt --output GCF_001202045.1_ASM120204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:35,190] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:35,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:35,191] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:35,202] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:35,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:35,203] [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
Pseudorhodobacter ferrugineus	strain=DSM 5888	GCA_000420745.1	77008	77008	type	True	99.986	1106	1122	95	conclusive
Pseudorhodobacter wandonensis	strain=KCTC 23672	GCA_001202035.1	1120568	1120568	type	True	81.4432	728	1122	95	below_threshold
Pseudorhodobacter antarcticus	strain=CGMCC 1.10836	GCA_900110135.1	1077947	1077947	type	True	80.5653	689	1122	95	below_threshold
Pseudorhodobacter antarcticus	strain=KCTC 23700	GCA_001202015.1	1077947	1077947	type	True	80.5565	673	1122	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	79.3698	510	1122	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.5855	351	1122	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.5579	350	1122	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	77.5029	344	1122	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.0028	272	1122	95	below_threshold
Celeribacter baekdonensis	strain=DSM 27375	GCA_900102315.1	875171	875171	type	True	76.8071	141	1122	95	below_threshold
Actibacterium mucosum	strain=KCTC 23349	GCA_000647975.1	1087332	1087332	type	True	76.6339	148	1122	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.6141	156	1122	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.4099	122	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:35,216] [INFO] DFAST Taxonomy check result was written to GCF_001202045.1_ASM120204v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:35,217] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:35,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:35,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/checkm_data
[2024-01-24 11:21:35,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:35,257] [INFO] Task started: CheckM
[2024-01-24 11:21:35,257] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001202045.1_ASM120204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001202045.1_ASM120204v1_genomic.fna/checkm_input GCF_001202045.1_ASM120204v1_genomic.fna/checkm_result
[2024-01-24 11:22:11,951] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:11,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:11,968] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:11,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:11,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001202045.1_ASM120204v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:11,970] [INFO] Task started: Blastn
[2024-01-24 11:22:11,970] [INFO] Running command: blastn -query GCF_001202045.1_ASM120204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81dbb207-a79a-4b0f-8a5d-ea88a123485c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001202045.1_ASM120204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:13,357] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:13,361] [INFO] Selected 10 target genomes.
[2024-01-24 11:22:13,361] [INFO] Target genome list was writen to GCF_001202045.1_ASM120204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:13,383] [INFO] Task started: fastANI
[2024-01-24 11:22:13,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgc161c6c7-aa74-4bdc-84b8-34ca2cb2dbb1/GCF_001202045.1_ASM120204v1_genomic.fna.gz --refList GCF_001202045.1_ASM120204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001202045.1_ASM120204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:21,146] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:21,163] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:21,164] [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_000420745.1	s__Pseudorhodobacter ferrugineus	99.986	1106	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001202035.1	s__Pseudorhodobacter wandonensis	81.4346	728	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	81.1814	785	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110135.1	s__Pseudorhodobacter antarcticus	80.5737	688	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_005234135.1	s__Pseudorhodobacter turbinis	79.3439	514	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001202025.1	s__Pseudorhodobacter aquimaris	79.136	488	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	77.6408	298	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773375.1	s__Cypionkella sp009773375	77.3978	309	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	77.2684	334	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008711135.1	s__LNNU-3342 sp008711135	76.4258	147	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LNNU-3342	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:21,165] [INFO] GTDB search result was written to GCF_001202045.1_ASM120204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:21,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:21,170] [INFO] DFAST_QC result json was written to GCF_001202045.1_ASM120204v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:21,171] [INFO] DFAST_QC completed!
[2024-01-24 11:22:21,171] [INFO] Total running time: 0h1m14s