[2024-01-25 19:31:51,435] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,436] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference
[2024-01-25 19:31:52,606] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,606] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg546a5770-a348-4cdf-8666-61e933635feb/GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna.gz | prodigal -d GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/cds.fna -a GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:31:59,382] [INFO] Task succeeded: Prodigal
[2024-01-25 19:31:59,383] [INFO] Task started: HMMsearch
[2024-01-25 19:31:59,383] [INFO] Running command: hmmsearch --tblout GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/reference_markers.hmm GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:31:59,578] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:31:59,579] [INFO] Found 6/6 markers.
[2024-01-25 19:31:59,609] [INFO] Query marker FASTA was written to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/markers.fasta
[2024-01-25 19:31:59,609] [INFO] Task started: Blastn
[2024-01-25 19:31:59,609] [INFO] Running command: blastn -query GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/reference_markers.fasta -out GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:00,260] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:00,263] [INFO] Selected 14 target genomes.
[2024-01-25 19:32:00,264] [INFO] Target genome list was writen to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:00,269] [INFO] Task started: fastANI
[2024-01-25 19:32:00,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg546a5770-a348-4cdf-8666-61e933635feb/GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna.gz --refList GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/target_genomes.txt --output GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:32:11,098] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:11,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:32:11,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:32:11,109] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:32:11,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:32:11,109] [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
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	99.9948	1140	1150	95	conclusive
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	99.9537	1098	1150	95	conclusive
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	83.5818	794	1150	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	83.5758	777	1150	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	83.4038	804	1150	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	83.3082	769	1150	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.2978	799	1150	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.2771	777	1150	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	83.2373	808	1150	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.902	749	1150	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.3002	494	1150	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.2994	513	1150	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.2808	503	1150	95	below_threshold
Acinetobacter soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	78.99	316	1150	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:32:11,110] [INFO] DFAST Taxonomy check result was written to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:32:11,111] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:32:11,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:32:11,111] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/checkm_data
[2024-01-25 19:32:11,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:32:11,148] [INFO] Task started: CheckM
[2024-01-25 19:32:11,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/checkm_input GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/checkm_result
[2024-01-25 19:32:36,387] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:36,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:36,405] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:36,406] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:36,406] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/markers.fasta)
[2024-01-25 19:32:36,406] [INFO] Task started: Blastn
[2024-01-25 19:32:36,406] [INFO] Running command: blastn -query GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96d8a175-6ed5-44b9-97bf-5a5ae8bbf2c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:37,447] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:37,450] [INFO] Selected 16 target genomes.
[2024-01-25 19:32:37,450] [INFO] Target genome list was writen to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:37,458] [INFO] Task started: fastANI
[2024-01-25 19:32:37,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg546a5770-a348-4cdf-8666-61e933635feb/GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna.gz --refList GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:50,521] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:50,532] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:50,533] [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_000368585.1	s__Acinetobacter venetianus	99.9948	1140	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	conclusive
GCF_009884975.1	s__Acinetobacter dispersus	83.7143	806	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369525.1	s__Acinetobacter sp000369525	83.6072	792	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000368765.1	s__Acinetobacter junii	83.5865	794	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_002165255.2	s__Acinetobacter sp002165255	83.515	700	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000400715.1	s__Acinetobacter sp000400715	83.44	801	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367945.1	s__Acinetobacter proteolyticus	83.4097	803	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_011753255.1	s__Acinetobacter sp011753255	83.3923	807	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	83.3137	768	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_014635885.1	s__Acinetobacter vivianii	83.2771	777	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	83.2479	807	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_013072695.1	s__Acinetobacter sp013072695	83.2463	807	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987695.1	s__Acinetobacter sp003987695	83.1749	683	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000369505.1	s__Acinetobacter sp000369505	82.4818	750	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_013009345.1	s__Acinetobacter sp013009345	80.3063	488	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	-
GCF_000760595.1	s__Acinetobacter soli	78.99	316	1150	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:50,534] [INFO] GTDB search result was written to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:50,535] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:50,539] [INFO] DFAST_QC result json was written to GCF_000368585.1_Acin_vene_CIP_110063_V1_genomic.fna/dqc_result.json
[2024-01-25 19:32:50,539] [INFO] DFAST_QC completed!
[2024-01-25 19:32:50,539] [INFO] Total running time: 0h0m59s