[2024-01-24 13:57:13,637] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,639] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,639] [INFO] DQC Reference Directory: /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference
[2024-01-24 13:57:14,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,949] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e55c961-8cbe-45c0-8066-1fef573bcf0e/GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna.gz | prodigal -d GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/cds.fna -a GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:22,241] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:22,242] [INFO] Task started: HMMsearch
[2024-01-24 13:57:22,242] [INFO] Running command: hmmsearch --tblout GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/reference_markers.hmm GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:22,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:22,509] [INFO] Found 6/6 markers.
[2024-01-24 13:57:22,539] [INFO] Query marker FASTA was written to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/markers.fasta
[2024-01-24 13:57:22,540] [INFO] Task started: Blastn
[2024-01-24 13:57:22,540] [INFO] Running command: blastn -query GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/markers.fasta -db /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/reference_markers.fasta -out GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:23,242] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:23,247] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:23,247] [INFO] Target genome list was writen to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/target_genomes.txt
[2024-01-24 13:57:23,251] [INFO] Task started: fastANI
[2024-01-24 13:57:23,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e55c961-8cbe-45c0-8066-1fef573bcf0e/GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna.gz --refList GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/target_genomes.txt --output GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:33,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:33,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:33,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:33,480] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:57:33,480] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:33,481] [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 haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	100.0	1041	1050	95	conclusive
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	99.9981	1046	1050	95	conclusive
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	99.9966	1048	1050	95	conclusive
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	99.9845	1046	1050	95	conclusive
Acinetobacter junii	strain=CIP 64.5	GCA_000368765.1	40215	40215	type	True	83.8063	689	1050	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	83.7121	694	1050	95	below_threshold
Acinetobacter modestus	strain=CCM 8639	GCA_014636095.1	1776740	1776740	type	True	82.8994	658	1050	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	82.8176	731	1050	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	82.7176	710	1050	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	82.6458	692	1050	95	below_threshold
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	82.4787	667	1050	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.2913	360	1050	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.983	337	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:33,482] [INFO] DFAST Taxonomy check result was written to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/tc_result.tsv
[2024-01-24 13:57:33,483] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:33,483] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:33,483] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/checkm_data
[2024-01-24 13:57:33,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:33,517] [INFO] Task started: CheckM
[2024-01-24 13:57:33,517] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/checkm_input GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/checkm_result
[2024-01-24 13:58:03,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:03,330] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,354] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:03,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:03,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/markers.fasta)
[2024-01-24 13:58:03,355] [INFO] Task started: Blastn
[2024-01-24 13:58:03,355] [INFO] Running command: blastn -query GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/markers.fasta -db /var/lib/cwl/stgac2b9b92-65cb-42a7-a637-d910296c959e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:04,524] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:04,528] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:04,529] [INFO] Target genome list was writen to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:04,538] [INFO] Task started: fastANI
[2024-01-24 13:58:04,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e55c961-8cbe-45c0-8066-1fef573bcf0e/GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna.gz --refList GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/target_genomes_gtdb.txt --output GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:18,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:18,791] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:18,791] [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_000369065.1	s__Acinetobacter haemolyticus	99.9845	1046	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	conclusive
GCF_008630915.1	s__Acinetobacter sp008630915	93.8393	887	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	92.7631	875	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368765.1	s__Acinetobacter junii	83.8063	689	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_002165255.2	s__Acinetobacter sp002165255	83.0894	628	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.92	96.70	0.85	0.83	6	-
GCF_014636095.1	s__Acinetobacter modestus	82.9084	657	1050	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	82.8895	709	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_000400715.1	s__Acinetobacter sp000400715	82.8703	707	1050	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	82.809	715	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_014635885.1	s__Acinetobacter vivianii	82.7678	687	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000367945.1	s__Acinetobacter proteolyticus	82.729	709	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_009884975.1	s__Acinetobacter dispersus	82.7264	709	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369805.1	s__Acinetobacter sp000369805	82.6982	693	1050	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	82.6458	692	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000369645.1	s__Acinetobacter sp000369645	82.5077	682	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_014635545.1	s__Acinetobacter courvalinii	82.3455	666	1050	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:18,796] [INFO] GTDB search result was written to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:18,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:18,801] [INFO] DFAST_QC result json was written to GCF_000430205.1_Acinetobacter_haemolyticus_genomic.fna/dqc_result.json
[2024-01-24 13:58:18,801] [INFO] DFAST_QC completed!
[2024-01-24 13:58:18,801] [INFO] Total running time: 0h1m5s