[2023-06-19 13:42:53,684] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:42:53,686] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:42:53,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference
[2023-06-19 13:42:55,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:42:55,282] [INFO] Task started: Prodigal
[2023-06-19 13:42:55,282] [INFO] Running command: gunzip -c /var/lib/cwl/stga296b8e2-56d7-4be4-a710-eb54df3be28c/GCA_018004035.1_ASM1800403v1_genomic.fna.gz | prodigal -d GCA_018004035.1_ASM1800403v1_genomic.fna/cds.fna -a GCA_018004035.1_ASM1800403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:42:58,462] [INFO] Task succeeded: Prodigal
[2023-06-19 13:42:58,462] [INFO] Task started: HMMsearch
[2023-06-19 13:42:58,462] [INFO] Running command: hmmsearch --tblout GCA_018004035.1_ASM1800403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/reference_markers.hmm GCA_018004035.1_ASM1800403v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:42:58,666] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:42:58,667] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga296b8e2-56d7-4be4-a710-eb54df3be28c/GCA_018004035.1_ASM1800403v1_genomic.fna.gz]
[2023-06-19 13:42:58,687] [INFO] Query marker FASTA was written to GCA_018004035.1_ASM1800403v1_genomic.fna/markers.fasta
[2023-06-19 13:42:58,688] [INFO] Task started: Blastn
[2023-06-19 13:42:58,688] [INFO] Running command: blastn -query GCA_018004035.1_ASM1800403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/reference_markers.fasta -out GCA_018004035.1_ASM1800403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:00,840] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:00,845] [INFO] Selected 13 target genomes.
[2023-06-19 13:43:00,846] [INFO] Target genome list was writen to GCA_018004035.1_ASM1800403v1_genomic.fna/target_genomes.txt
[2023-06-19 13:43:00,857] [INFO] Task started: fastANI
[2023-06-19 13:43:00,858] [INFO] Running command: fastANI --query /var/lib/cwl/stga296b8e2-56d7-4be4-a710-eb54df3be28c/GCA_018004035.1_ASM1800403v1_genomic.fna.gz --refList GCA_018004035.1_ASM1800403v1_genomic.fna/target_genomes.txt --output GCA_018004035.1_ASM1800403v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:43:08,085] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:08,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:43:08,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:43:08,103] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:43:08,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:43:08,103] [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 halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	93.1582	271	444	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	83.5623	256	444	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	81.455	197	444	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	81.099	209	444	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	81.0951	205	444	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	81.0707	203	444	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	80.9567	192	444	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	80.6992	163	444	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	80.5871	158	444	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	80.3017	213	444	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	78.6868	111	444	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	78.4119	67	444	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	77.9962	94	444	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:43:08,105] [INFO] DFAST Taxonomy check result was written to GCA_018004035.1_ASM1800403v1_genomic.fna/tc_result.tsv
[2023-06-19 13:43:08,106] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:43:08,106] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:43:08,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/checkm_data
[2023-06-19 13:43:08,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:43:08,128] [INFO] Task started: CheckM
[2023-06-19 13:43:08,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018004035.1_ASM1800403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018004035.1_ASM1800403v1_genomic.fna/checkm_input GCA_018004035.1_ASM1800403v1_genomic.fna/checkm_result
[2023-06-19 13:43:25,905] [INFO] Task succeeded: CheckM
[2023-06-19 13:43:25,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 8.33%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-19 13:43:25,927] [INFO] ===== Completeness check finished =====
[2023-06-19 13:43:25,928] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:43:25,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018004035.1_ASM1800403v1_genomic.fna/markers.fasta)
[2023-06-19 13:43:25,928] [INFO] Task started: Blastn
[2023-06-19 13:43:25,928] [INFO] Running command: blastn -query GCA_018004035.1_ASM1800403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg862f0820-68bc-4153-b703-f125982e43cb/dqc_reference/reference_markers_gtdb.fasta -out GCA_018004035.1_ASM1800403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:43:26,441] [INFO] Task succeeded: Blastn
[2023-06-19 13:43:26,446] [INFO] Selected 11 target genomes.
[2023-06-19 13:43:26,446] [INFO] Target genome list was writen to GCA_018004035.1_ASM1800403v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:43:26,452] [INFO] Task started: fastANI
[2023-06-19 13:43:26,452] [INFO] Running command: fastANI --query /var/lib/cwl/stga296b8e2-56d7-4be4-a710-eb54df3be28c/GCA_018004035.1_ASM1800403v1_genomic.fna.gz --refList GCA_018004035.1_ASM1800403v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018004035.1_ASM1800403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:43:33,150] [INFO] Task succeeded: fastANI
[2023-06-19 13:43:33,162] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 13:43:33,162] [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_000369505.1	s__Acinetobacter sp000369505	94.8907	289	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_004208515.1	s__Acinetobacter halotolerans	93.1582	271	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
GCA_003987695.1	s__Acinetobacter sp003987695	81.195	169	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_002165255.2	s__Acinetobacter sp002165255	81.1619	171	444	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	81.1158	203	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	-
GCF_000400715.1	s__Acinetobacter sp000400715	80.9133	234	444	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	80.7696	236	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000369405.1	s__Acinetobacter sp000369405	80.669	227	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009884975.1	s__Acinetobacter dispersus	80.5704	212	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000368925.1	s__Acinetobacter bereziniae	77.5677	108	444	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.33	97.29	0.90	0.83	53	-
--------------------------------------------------------------------------------
[2023-06-19 13:43:33,164] [INFO] GTDB search result was written to GCA_018004035.1_ASM1800403v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:43:33,165] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:43:33,169] [INFO] DFAST_QC result json was written to GCA_018004035.1_ASM1800403v1_genomic.fna/dqc_result.json
[2023-06-19 13:43:33,170] [INFO] DFAST_QC completed!
[2023-06-19 13:43:33,170] [INFO] Total running time: 0h0m39s