[2024-01-24 13:37:04,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference
[2024-01-24 13:37:06,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,397] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bf9eca1-2443-407a-93f5-b7748cdac1e5/GCF_022601685.1_ASM2260168v1_genomic.fna.gz | prodigal -d GCF_022601685.1_ASM2260168v1_genomic.fna/cds.fna -a GCF_022601685.1_ASM2260168v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:12,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:12,922] [INFO] Task started: HMMsearch
[2024-01-24 13:37:12,923] [INFO] Running command: hmmsearch --tblout GCF_022601685.1_ASM2260168v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/reference_markers.hmm GCF_022601685.1_ASM2260168v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:13,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:13,187] [INFO] Found 6/6 markers.
[2024-01-24 13:37:13,208] [INFO] Query marker FASTA was written to GCF_022601685.1_ASM2260168v1_genomic.fna/markers.fasta
[2024-01-24 13:37:13,208] [INFO] Task started: Blastn
[2024-01-24 13:37:13,209] [INFO] Running command: blastn -query GCF_022601685.1_ASM2260168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/reference_markers.fasta -out GCF_022601685.1_ASM2260168v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:13,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:13,932] [INFO] Selected 31 target genomes.
[2024-01-24 13:37:13,933] [INFO] Target genome list was writen to GCF_022601685.1_ASM2260168v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:13,958] [INFO] Task started: fastANI
[2024-01-24 13:37:13,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf9eca1-2443-407a-93f5-b7748cdac1e5/GCF_022601685.1_ASM2260168v1_genomic.fna.gz --refList GCF_022601685.1_ASM2260168v1_genomic.fna/target_genomes.txt --output GCF_022601685.1_ASM2260168v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:30,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:30,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:30,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:30,545] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:30,545] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:30,545] [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 johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	78.8746	185	822	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.7695	194	822	95	below_threshold
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	78.7546	196	822	95	below_threshold
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	78.6865	172	822	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	78.5443	144	822	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	78.5115	184	822	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.5071	149	822	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	78.507	149	822	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_009035845.1	470	470	type	True	78.5053	144	822	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	78.4597	151	822	95	below_threshold
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	78.4217	160	822	95	below_threshold
Acinetobacter chinensis	strain=WCHAc010005	GCA_002165375.2	2004650	2004650	type	True	78.4054	160	822	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	78.382	190	822	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	78.3726	178	822	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.3509	195	822	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	78.3466	183	822	95	below_threshold
Acinetobacter tandoii	strain=DSM 14970	GCA_000621065.1	202954	202954	type	True	78.3428	178	822	95	below_threshold
Acinetobacter brisouii	strain=CIP 110357	GCA_000488275.1	396323	396323	type	True	78.3148	178	822	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.3071	188	822	95	below_threshold
Acinetobacter brisouii	strain=DSM 18516	GCA_000931655.1	396323	396323	type	True	78.2509	176	822	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	78.2486	184	822	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.135	187	822	95	below_threshold
Acinetobacter populi	strain=PBJ7	GCA_002174125.1	1582270	1582270	type	True	78.1142	248	822	95	below_threshold
Acinetobacter baretiae	strain=B10A	GCA_015627105.1	2605383	2605383	type	True	77.9896	89	822	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	77.9857	162	822	95	below_threshold
Acinetobacter pittii	strain=CIP 70.29	GCA_000369045.1	48296	48296	type	True	77.9788	157	822	95	below_threshold
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	77.9264	171	822	95	below_threshold
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	77.8218	165	822	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:30,547] [INFO] DFAST Taxonomy check result was written to GCF_022601685.1_ASM2260168v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:30,547] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:30,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:30,548] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/checkm_data
[2024-01-24 13:37:30,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:30,577] [INFO] Task started: CheckM
[2024-01-24 13:37:30,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022601685.1_ASM2260168v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022601685.1_ASM2260168v1_genomic.fna/checkm_input GCF_022601685.1_ASM2260168v1_genomic.fna/checkm_result
[2024-01-24 13:37:58,910] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:58,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:58,925] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:58,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:58,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022601685.1_ASM2260168v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:58,926] [INFO] Task started: Blastn
[2024-01-24 13:37:58,926] [INFO] Running command: blastn -query GCF_022601685.1_ASM2260168v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e67436f-9e95-4bf2-8c73-d71eb1475724/dqc_reference/reference_markers_gtdb.fasta -out GCF_022601685.1_ASM2260168v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:00,075] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:00,084] [INFO] Selected 15 target genomes.
[2024-01-24 13:38:00,084] [INFO] Target genome list was writen to GCF_022601685.1_ASM2260168v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:00,104] [INFO] Task started: fastANI
[2024-01-24 13:38:00,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf9eca1-2443-407a-93f5-b7748cdac1e5/GCF_022601685.1_ASM2260168v1_genomic.fna.gz --refList GCF_022601685.1_ASM2260168v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022601685.1_ASM2260168v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:09,833] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:09,850] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:38:09,851] [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
GCA_001626925.1	s__Acinetobacter sp001626925	91.3281	653	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.78	99.66	0.96	0.94	7	-
GCF_900096915.1	s__Acinetobacter marinus	86.0421	634	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336635.1	s__Acinetobacter sp004336635	78.6973	159	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_009759685.1	s__Acinetobacter baumannii	78.4593	148	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	-
GCF_013004375.1	s__Acinetobacter terrae	78.3939	177	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_003268395.1	s__Acinetobacter sp003268395	78.3701	234	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012371325.1	s__Acinetobacter sp012371325	78.3142	181	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.91	97.28	0.89	0.84	6	-
GCF_000368265.1	s__Acinetobacter sp000368265	78.2908	165	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.84	96.49	0.89	0.85	3	-
GCF_001612555.1	s__Acinetobacter sp001612555	78.2224	174	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003987695.1	s__Acinetobacter sp003987695	78.1627	184	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_900096995.1	s__Acinetobacter puyangensis	78.1376	245	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002174125.1	s__Acinetobacter populi	78.1197	247	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008017315.1	s__Acinetobacter sp008017315	78.0834	210	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008693185.1	s__Acinetobacter qingfengensis	78.0775	191	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009372215.1	s__Acinetobacter portensis	77.9857	162	822	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:09,852] [INFO] GTDB search result was written to GCF_022601685.1_ASM2260168v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:09,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:09,857] [INFO] DFAST_QC result json was written to GCF_022601685.1_ASM2260168v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:09,857] [INFO] DFAST_QC completed!
[2024-01-24 13:38:09,857] [INFO] Total running time: 0h1m5s