[2024-01-25 18:14:20,761] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:14:20,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:14:20,763] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference
[2024-01-25 18:14:21,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:14:21,895] [INFO] Task started: Prodigal
[2024-01-25 18:14:21,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b65cea1-be5f-4084-93ed-30979c17dc03/GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna.gz | prodigal -d GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/cds.fna -a GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:14:28,754] [INFO] Task succeeded: Prodigal
[2024-01-25 18:14:28,754] [INFO] Task started: HMMsearch
[2024-01-25 18:14:28,754] [INFO] Running command: hmmsearch --tblout GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/reference_markers.hmm GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:14:28,984] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:14:28,985] [INFO] Found 6/6 markers.
[2024-01-25 18:14:29,014] [INFO] Query marker FASTA was written to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/markers.fasta
[2024-01-25 18:14:29,015] [INFO] Task started: Blastn
[2024-01-25 18:14:29,015] [INFO] Running command: blastn -query GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/reference_markers.fasta -out GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:29,680] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:29,683] [INFO] Selected 19 target genomes.
[2024-01-25 18:14:29,683] [INFO] Target genome list was writen to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/target_genomes.txt
[2024-01-25 18:14:29,692] [INFO] Task started: fastANI
[2024-01-25 18:14:29,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b65cea1-be5f-4084-93ed-30979c17dc03/GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna.gz --refList GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/target_genomes.txt --output GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:14:44,017] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:44,017] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:14:44,017] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:14:44,029] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:14:44,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:14:44,030] [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 junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	85.2157	782	1186	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	84.434	814	1186	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	84.3727	797	1186	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	84.3654	810	1186	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	84.3082	816	1186	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	84.0789	762	1186	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.5013	810	1186	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.4874	826	1186	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	83.4647	834	1186	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	83.4582	836	1186	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	83.4276	802	1186	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.4073	836	1186	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.2838	762	1186	95	below_threshold
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	82.7244	746	1186	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	82.6634	755	1186	95	below_threshold
Acinetobacter halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	82.6497	761	1186	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.135	500	1186	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.1113	509	1186	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.1068	495	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:14:44,031] [INFO] DFAST Taxonomy check result was written to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/tc_result.tsv
[2024-01-25 18:14:44,032] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:14:44,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:14:44,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/checkm_data
[2024-01-25 18:14:44,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:14:44,072] [INFO] Task started: CheckM
[2024-01-25 18:14:44,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/checkm_input GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/checkm_result
[2024-01-25 18:15:09,559] [INFO] Task succeeded: CheckM
[2024-01-25 18:15:09,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:15:09,581] [INFO] ===== Completeness check finished =====
[2024-01-25 18:15:09,581] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:15:09,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/markers.fasta)
[2024-01-25 18:15:09,582] [INFO] Task started: Blastn
[2024-01-25 18:15:09,582] [INFO] Running command: blastn -query GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6136fe6-67f8-481b-a401-ee574e0dbeb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:10,637] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:10,641] [INFO] Selected 15 target genomes.
[2024-01-25 18:15:10,641] [INFO] Target genome list was writen to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:15:10,659] [INFO] Task started: fastANI
[2024-01-25 18:15:10,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b65cea1-be5f-4084-93ed-30979c17dc03/GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna.gz --refList GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:23,292] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:23,302] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:23,302] [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_000369005.1	s__Acinetobacter beijerinckii	99.9965	1183	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	84.5226	730	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_014636095.1	s__Acinetobacter modestus	84.434	814	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	84.3654	810	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCF_009884975.1	s__Acinetobacter dispersus	84.1285	838	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000400715.1	s__Acinetobacter sp000400715	84.1172	832	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369405.1	s__Acinetobacter sp000369405	84.0666	830	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369525.1	s__Acinetobacter sp000369525	84.0	844	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCA_003987695.1	s__Acinetobacter sp003987695	83.9456	699	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000369805.1	s__Acinetobacter sp000369805	83.8602	837	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011753255.1	s__Acinetobacter sp011753255	83.7635	829	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	83.4737	832	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000368585.1	s__Acinetobacter venetianus	83.4617	827	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_000367945.1	s__Acinetobacter proteolyticus	83.452	837	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_004208515.1	s__Acinetobacter halotolerans	82.6595	760	1186	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:23,303] [INFO] GTDB search result was written to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:23,304] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:23,307] [INFO] DFAST_QC result json was written to GCF_000369005.1_Acin_beij_CIP_110307_V1_genomic.fna/dqc_result.json
[2024-01-25 18:15:23,307] [INFO] DFAST_QC completed!
[2024-01-25 18:15:23,307] [INFO] Total running time: 0h1m3s