[2024-01-24 14:28:07,944] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:07,945] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:07,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference
[2024-01-24 14:28:10,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:10,418] [INFO] Task started: Prodigal
[2024-01-24 14:28:10,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b3cc1bb-d6b7-4637-9668-aeb1b30350d6/GCF_004208515.1_ASM420851v1_genomic.fna.gz | prodigal -d GCF_004208515.1_ASM420851v1_genomic.fna/cds.fna -a GCF_004208515.1_ASM420851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:18,740] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:18,741] [INFO] Task started: HMMsearch
[2024-01-24 14:28:18,741] [INFO] Running command: hmmsearch --tblout GCF_004208515.1_ASM420851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/reference_markers.hmm GCF_004208515.1_ASM420851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:19,050] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:19,052] [INFO] Found 6/6 markers.
[2024-01-24 14:28:19,093] [INFO] Query marker FASTA was written to GCF_004208515.1_ASM420851v1_genomic.fna/markers.fasta
[2024-01-24 14:28:19,093] [INFO] Task started: Blastn
[2024-01-24 14:28:19,094] [INFO] Running command: blastn -query GCF_004208515.1_ASM420851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/reference_markers.fasta -out GCF_004208515.1_ASM420851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:19,937] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:19,953] [INFO] Selected 21 target genomes.
[2024-01-24 14:28:19,954] [INFO] Target genome list was writen to GCF_004208515.1_ASM420851v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:20,027] [INFO] Task started: fastANI
[2024-01-24 14:28:20,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3cc1bb-d6b7-4637-9668-aeb1b30350d6/GCF_004208515.1_ASM420851v1_genomic.fna.gz --refList GCF_004208515.1_ASM420851v1_genomic.fna/target_genomes.txt --output GCF_004208515.1_ASM420851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:36,424] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:36,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:36,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:36,441] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:36,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:36,442] [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	100.0	1082	1082	95	conclusive
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	83.9649	795	1082	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	83.9149	830	1082	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	83.8585	828	1082	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	83.7966	843	1082	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	82.646	709	1082	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	82.5979	710	1082	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000759995.1	202955	202955	type	True	82.5972	707	1082	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	82.5405	697	1082	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	82.3878	743	1082	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	82.3728	732	1082	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	82.3411	741	1082	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	82.3177	737	1082	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	82.2979	725	1082	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	82.2687	708	1082	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.2173	679	1082	95	below_threshold
Acinetobacter parvus	strain=DSM 16617	GCA_000248155.2	134533	134533	type	True	82.0705	560	1082	95	below_threshold
Acinetobacter parvus	strain=CIP 108168	GCA_000368025.1	134533	134533	type	True	82.0353	587	1082	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.7761	462	1082	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.7271	467	1082	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.2762	358	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:36,446] [INFO] DFAST Taxonomy check result was written to GCF_004208515.1_ASM420851v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:36,446] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:36,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:36,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/checkm_data
[2024-01-24 14:28:36,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:36,485] [INFO] Task started: CheckM
[2024-01-24 14:28:36,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004208515.1_ASM420851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004208515.1_ASM420851v1_genomic.fna/checkm_input GCF_004208515.1_ASM420851v1_genomic.fna/checkm_result
[2024-01-24 14:29:07,900] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:07,901] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:07,920] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:07,921] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:07,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004208515.1_ASM420851v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:07,921] [INFO] Task started: Blastn
[2024-01-24 14:29:07,921] [INFO] Running command: blastn -query GCF_004208515.1_ASM420851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61b3eabf-2832-472f-a589-5083650aadcd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004208515.1_ASM420851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:09,068] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:09,072] [INFO] Selected 13 target genomes.
[2024-01-24 14:29:09,072] [INFO] Target genome list was writen to GCF_004208515.1_ASM420851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:09,096] [INFO] Task started: fastANI
[2024-01-24 14:29:09,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b3cc1bb-d6b7-4637-9668-aeb1b30350d6/GCF_004208515.1_ASM420851v1_genomic.fna.gz --refList GCF_004208515.1_ASM420851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004208515.1_ASM420851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:22,104] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:22,116] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:22,116] [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_004208515.1	s__Acinetobacter halotolerans	100.0	1082	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	conclusive
GCF_000369505.1	s__Acinetobacter sp000369505	93.3141	949	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_000369065.1	s__Acinetobacter haemolyticus	83.9149	830	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	83.7068	828	1082	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	82.8032	636	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_000369805.1	s__Acinetobacter sp000369805	82.7295	733	1082	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	82.6256	748	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369005.1	s__Acinetobacter beijerinckii	82.5704	749	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.53	96.54	0.91	0.85	5	-
GCF_000400715.1	s__Acinetobacter sp000400715	82.4548	746	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013072695.1	s__Acinetobacter sp013072695	82.4343	744	1082	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	82.429	754	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165255.2	s__Acinetobacter sp002165255	82.4038	640	1082	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_014635885.1	s__Acinetobacter vivianii	82.3177	737	1082	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 14:29:22,118] [INFO] GTDB search result was written to GCF_004208515.1_ASM420851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:22,119] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:22,124] [INFO] DFAST_QC result json was written to GCF_004208515.1_ASM420851v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:22,124] [INFO] DFAST_QC completed!
[2024-01-24 14:29:22,124] [INFO] Total running time: 0h1m14s