[2024-01-25 19:36:51,022] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:51,026] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:51,026] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference
[2024-01-25 19:36:52,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:52,235] [INFO] Task started: Prodigal
[2024-01-25 19:36:52,236] [INFO] Running command: gunzip -c /var/lib/cwl/stg96d15b4e-7bf7-4052-a79f-23dd076a0d79/GCF_900444875.1_46338_C01_genomic.fna.gz | prodigal -d GCF_900444875.1_46338_C01_genomic.fna/cds.fna -a GCF_900444875.1_46338_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:58,730] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:58,730] [INFO] Task started: HMMsearch
[2024-01-25 19:36:58,730] [INFO] Running command: hmmsearch --tblout GCF_900444875.1_46338_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/reference_markers.hmm GCF_900444875.1_46338_C01_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:58,967] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:58,968] [INFO] Found 6/6 markers.
[2024-01-25 19:36:58,994] [INFO] Query marker FASTA was written to GCF_900444875.1_46338_C01_genomic.fna/markers.fasta
[2024-01-25 19:36:58,995] [INFO] Task started: Blastn
[2024-01-25 19:36:58,995] [INFO] Running command: blastn -query GCF_900444875.1_46338_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/reference_markers.fasta -out GCF_900444875.1_46338_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:59,588] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:59,590] [INFO] Selected 16 target genomes.
[2024-01-25 19:36:59,591] [INFO] Target genome list was writen to GCF_900444875.1_46338_C01_genomic.fna/target_genomes.txt
[2024-01-25 19:36:59,593] [INFO] Task started: fastANI
[2024-01-25 19:36:59,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d15b4e-7bf7-4052-a79f-23dd076a0d79/GCF_900444875.1_46338_C01_genomic.fna.gz --refList GCF_900444875.1_46338_C01_genomic.fna/target_genomes.txt --output GCF_900444875.1_46338_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:11,367] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:11,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:11,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:11,377] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:37:11,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:11,377] [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	100.0	1116	1119	95	conclusive
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	99.9575	1106	1119	95	conclusive
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	84.3221	588	1119	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	84.2762	617	1119	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	83.9691	712	1119	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	83.9539	711	1119	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	83.9292	730	1119	95	below_threshold
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	83.7135	677	1119	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.6415	762	1119	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	83.5888	779	1119	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	82.6403	724	1119	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	82.5858	730	1119	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	82.5602	728	1119	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	80.7454	464	1119	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	80.6733	466	1119	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.5527	487	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:11,380] [INFO] DFAST Taxonomy check result was written to GCF_900444875.1_46338_C01_genomic.fna/tc_result.tsv
[2024-01-25 19:37:11,380] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:11,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:11,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/checkm_data
[2024-01-25 19:37:11,381] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:11,416] [INFO] Task started: CheckM
[2024-01-25 19:37:11,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900444875.1_46338_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900444875.1_46338_C01_genomic.fna/checkm_input GCF_900444875.1_46338_C01_genomic.fna/checkm_result
[2024-01-25 19:37:35,807] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:35,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:35,820] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:35,820] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:35,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900444875.1_46338_C01_genomic.fna/markers.fasta)
[2024-01-25 19:37:35,821] [INFO] Task started: Blastn
[2024-01-25 19:37:35,821] [INFO] Running command: blastn -query GCF_900444875.1_46338_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bc1b4c8-e29b-47ee-a01d-30ed2af71c7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900444875.1_46338_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:36,677] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:36,679] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:36,680] [INFO] Target genome list was writen to GCF_900444875.1_46338_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:36,686] [INFO] Task started: fastANI
[2024-01-25 19:37:36,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg96d15b4e-7bf7-4052-a79f-23dd076a0d79/GCF_900444875.1_46338_C01_genomic.fna.gz --refList GCF_900444875.1_46338_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900444875.1_46338_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:51,088] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:51,099] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:51,099] [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_000368765.1	s__Acinetobacter junii	99.9575	1106	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	conclusive
GCF_002165255.2	s__Acinetobacter sp002165255	85.8194	698	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_000369005.1	s__Acinetobacter beijerinckii	85.084	801	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000368025.1	s__Acinetobacter parvus	84.2588	619	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	96.79	0.91	0.83	11	-
GCF_000369065.1	s__Acinetobacter haemolyticus	83.9433	713	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
GCF_014636095.1	s__Acinetobacter modestus	83.9245	727	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_000368585.1	s__Acinetobacter venetianus	83.6238	776	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCA_003987695.1	s__Acinetobacter sp003987695	83.1937	674	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_011753255.1	s__Acinetobacter sp011753255	82.8353	713	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400715.1	s__Acinetobacter sp000400715	82.7307	733	1119	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	82.7297	737	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000367945.1	s__Acinetobacter proteolyticus	82.6496	725	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	82.5992	725	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000369645.1	s__Acinetobacter sp000369645	82.5853	692	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_014635885.1	s__Acinetobacter vivianii	82.5146	687	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_011058205.1	s__Acinetobacter fasciculus	80.1207	282	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCF_009557235.1	s__Acinetobacter wanghuae	79.556	299	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
GCA_002296655.1	s__Acinetobacter sp002296655	79.3285	295	1119	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:51,100] [INFO] GTDB search result was written to GCF_900444875.1_46338_C01_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:51,101] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:51,104] [INFO] DFAST_QC result json was written to GCF_900444875.1_46338_C01_genomic.fna/dqc_result.json
[2024-01-25 19:37:51,104] [INFO] DFAST_QC completed!
[2024-01-25 19:37:51,104] [INFO] Total running time: 0h1m0s