[2024-01-25 20:20:50,430] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:20:50,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:20:50,431] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference
[2024-01-25 20:20:51,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:20:51,548] [INFO] Task started: Prodigal
[2024-01-25 20:20:51,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg13d59955-6525-434b-97d8-0e70c2022f11/GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna.gz | prodigal -d GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/cds.fna -a GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:20:58,382] [INFO] Task succeeded: Prodigal
[2024-01-25 20:20:58,382] [INFO] Task started: HMMsearch
[2024-01-25 20:20:58,382] [INFO] Running command: hmmsearch --tblout GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/reference_markers.hmm GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:20:58,598] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:20:58,599] [INFO] Found 6/6 markers.
[2024-01-25 20:20:58,628] [INFO] Query marker FASTA was written to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/markers.fasta
[2024-01-25 20:20:58,628] [INFO] Task started: Blastn
[2024-01-25 20:20:58,628] [INFO] Running command: blastn -query GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/reference_markers.fasta -out GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:59,269] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:59,271] [INFO] Selected 18 target genomes.
[2024-01-25 20:20:59,272] [INFO] Target genome list was writen to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/target_genomes.txt
[2024-01-25 20:20:59,283] [INFO] Task started: fastANI
[2024-01-25 20:20:59,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d59955-6525-434b-97d8-0e70c2022f11/GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna.gz --refList GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/target_genomes.txt --output GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:13,804] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:13,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:13,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:13,816] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:21:13,816] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:21:13,816] [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 modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	99.9879	1160	1172	95	conclusive
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	88.1071	926	1172	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	88.0215	937	1172	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	87.9832	925	1172	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	85.6333	661	1172	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	85.5649	631	1172	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	84.4918	833	1172	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	84.4904	795	1172	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	84.4701	791	1172	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	84.1219	785	1172	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	84.1094	750	1172	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	84.0154	741	1172	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.6209	749	1172	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.4822	784	1172	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.925	696	1172	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.358	477	1172	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.3568	496	1172	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.2594	494	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:13,820] [INFO] DFAST Taxonomy check result was written to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:13,821] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:13,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:13,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/checkm_data
[2024-01-25 20:21:13,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:13,858] [INFO] Task started: CheckM
[2024-01-25 20:21:13,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/checkm_input GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/checkm_result
[2024-01-25 20:21:38,633] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:38,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:38,650] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:38,651] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:38,651] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/markers.fasta)
[2024-01-25 20:21:38,651] [INFO] Task started: Blastn
[2024-01-25 20:21:38,651] [INFO] Running command: blastn -query GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6ec9512-44bd-4ea0-b8c6-85ec9b271404/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:39,684] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:39,687] [INFO] Selected 15 target genomes.
[2024-01-25 20:21:39,687] [INFO] Target genome list was writen to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:39,705] [INFO] Task started: fastANI
[2024-01-25 20:21:39,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d59955-6525-434b-97d8-0e70c2022f11/GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna.gz --refList GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:52,049] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:52,059] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:52,060] [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_014636095.1	s__Acinetobacter modestus	99.9879	1160	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	94.6569	850	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000374425.1	s__Acinetobacter tjernbergiae	88.0215	937	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCA_003987695.1	s__Acinetobacter sp003987695	87.8103	774	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000368025.1	s__Acinetobacter parvus	85.6669	663	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_013072695.1	s__Acinetobacter sp013072695	84.498	837	1172	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	84.4916	832	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000369005.1	s__Acinetobacter beijerinckii	84.4884	802	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	84.4663	797	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_011753255.1	s__Acinetobacter sp011753255	84.4034	814	1172	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	84.3836	842	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000369805.1	s__Acinetobacter sp000369805	84.3435	814	1172	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	84.3259	800	1172	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	84.1256	784	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000369645.1	s__Acinetobacter sp000369645	84.0771	792	1172	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:52,061] [INFO] GTDB search result was written to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:52,062] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:52,066] [INFO] DFAST_QC result json was written to GCF_000367965.1_Acin_sp_NIPH_236_V1_genomic.fna/dqc_result.json
[2024-01-25 20:21:52,066] [INFO] DFAST_QC completed!
[2024-01-25 20:21:52,066] [INFO] Total running time: 0h1m2s