[2024-01-24 13:40:46,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,043] [INFO] DQC Reference Directory: /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference
[2024-01-24 13:40:47,347] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,348] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,348] [INFO] Running command: gunzip -c /var/lib/cwl/stg200b5ae3-369d-4787-9449-9078ca646cba/GCF_000759995.1_ASM75999v1_genomic.fna.gz | prodigal -d GCF_000759995.1_ASM75999v1_genomic.fna/cds.fna -a GCF_000759995.1_ASM75999v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:55,407] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:55,408] [INFO] Task started: HMMsearch
[2024-01-24 13:40:55,408] [INFO] Running command: hmmsearch --tblout GCF_000759995.1_ASM75999v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/reference_markers.hmm GCF_000759995.1_ASM75999v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,692] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,693] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,725] [INFO] Query marker FASTA was written to GCF_000759995.1_ASM75999v1_genomic.fna/markers.fasta
[2024-01-24 13:40:55,726] [INFO] Task started: Blastn
[2024-01-24 13:40:55,726] [INFO] Running command: blastn -query GCF_000759995.1_ASM75999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/reference_markers.fasta -out GCF_000759995.1_ASM75999v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,435] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,438] [INFO] Selected 15 target genomes.
[2024-01-24 13:40:56,438] [INFO] Target genome list was writen to GCF_000759995.1_ASM75999v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,455] [INFO] Task started: fastANI
[2024-01-24 13:40:56,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg200b5ae3-369d-4787-9449-9078ca646cba/GCF_000759995.1_ASM75999v1_genomic.fna.gz --refList GCF_000759995.1_ASM75999v1_genomic.fna/target_genomes.txt --output GCF_000759995.1_ASM75999v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:07,801] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:07,802] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:07,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,818] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:07,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:07,819] [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 tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	100.0	1196	1197	95	conclusive
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	99.9886	1191	1197	95	conclusive
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	99.9798	1169	1197	95	conclusive
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	88.0675	920	1197	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	83.7619	642	1197	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	83.7558	796	1197	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	83.7038	820	1197	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	83.6912	807	1197	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	83.463	751	1197	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	83.2088	761	1197	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.9794	748	1197	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.7066	706	1197	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.9207	497	1197	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.2919	401	1197	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.1336	400	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,823] [INFO] DFAST Taxonomy check result was written to GCF_000759995.1_ASM75999v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,823] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,823] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/checkm_data
[2024-01-24 13:41:07,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,866] [INFO] Task started: CheckM
[2024-01-24 13:41:07,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000759995.1_ASM75999v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000759995.1_ASM75999v1_genomic.fna/checkm_input GCF_000759995.1_ASM75999v1_genomic.fna/checkm_result
[2024-01-24 13:41:38,139] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:38,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,158] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:38,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:38,159] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000759995.1_ASM75999v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:38,159] [INFO] Task started: Blastn
[2024-01-24 13:41:38,159] [INFO] Running command: blastn -query GCF_000759995.1_ASM75999v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb81551b5-46a0-4964-99af-6085a740fc0f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000759995.1_ASM75999v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:39,229] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:39,234] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:39,234] [INFO] Target genome list was writen to GCF_000759995.1_ASM75999v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:39,295] [INFO] Task started: fastANI
[2024-01-24 13:41:39,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg200b5ae3-369d-4787-9449-9078ca646cba/GCF_000759995.1_ASM75999v1_genomic.fna.gz --refList GCF_000759995.1_ASM75999v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000759995.1_ASM75999v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:50,274] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,288] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:50,288] [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_000374425.1	s__Acinetobacter tjernbergiae	99.9886	1191	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.99	97.83	0.97	0.93	5	conclusive
GCA_003987695.1	s__Acinetobacter sp003987695	94.8207	828	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_014636095.1	s__Acinetobacter modestus	88.0688	920	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.76	96.94	0.90	0.86	5	-
GCF_002165255.2	s__Acinetobacter sp002165255	87.565	814	1197	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	84.3674	806	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369005.1	s__Acinetobacter beijerinckii	84.3506	817	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_009884975.1	s__Acinetobacter dispersus	84.0831	805	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369405.1	s__Acinetobacter sp000369405	83.9232	814	1197	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	83.7577	796	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000369805.1	s__Acinetobacter sp000369805	83.7271	810	1197	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	83.7266	798	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_000367945.1	s__Acinetobacter proteolyticus	83.7201	818	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_014635885.1	s__Acinetobacter vivianii	83.463	751	1197	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,290] [INFO] GTDB search result was written to GCF_000759995.1_ASM75999v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:50,290] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:50,294] [INFO] DFAST_QC result json was written to GCF_000759995.1_ASM75999v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:50,294] [INFO] DFAST_QC completed!
[2024-01-24 13:41:50,294] [INFO] Total running time: 0h1m4s