[2024-01-25 19:36:50,722] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:50,723] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:50,723] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference
[2024-01-25 19:36:51,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:51,866] [INFO] Task started: Prodigal
[2024-01-25 19:36:51,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgb162d319-aaaf-45ee-bdec-3e08ef46745a/GCF_016027055.1_ASM1602705v1_genomic.fna.gz | prodigal -d GCF_016027055.1_ASM1602705v1_genomic.fna/cds.fna -a GCF_016027055.1_ASM1602705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:59,577] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:59,578] [INFO] Task started: HMMsearch
[2024-01-25 19:36:59,578] [INFO] Running command: hmmsearch --tblout GCF_016027055.1_ASM1602705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/reference_markers.hmm GCF_016027055.1_ASM1602705v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:59,800] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:59,802] [INFO] Found 6/6 markers.
[2024-01-25 19:36:59,832] [INFO] Query marker FASTA was written to GCF_016027055.1_ASM1602705v1_genomic.fna/markers.fasta
[2024-01-25 19:36:59,832] [INFO] Task started: Blastn
[2024-01-25 19:36:59,832] [INFO] Running command: blastn -query GCF_016027055.1_ASM1602705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/reference_markers.fasta -out GCF_016027055.1_ASM1602705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:00,441] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:00,443] [INFO] Selected 13 target genomes.
[2024-01-25 19:37:00,444] [INFO] Target genome list was writen to GCF_016027055.1_ASM1602705v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:00,447] [INFO] Task started: fastANI
[2024-01-25 19:37:00,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgb162d319-aaaf-45ee-bdec-3e08ef46745a/GCF_016027055.1_ASM1602705v1_genomic.fna.gz --refList GCF_016027055.1_ASM1602705v1_genomic.fna/target_genomes.txt --output GCF_016027055.1_ASM1602705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:11,493] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:11,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:11,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:11,502] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 19:37:11,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:11,502] [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=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	100.0	1202	1204	95	conclusive
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	99.9998	1201	1204	95	conclusive
Acinetobacter johnsonii	strain=CIP 64.6	GCA_000368045.1	40214	40214	suspected-type	True	99.972	1188	1204	95	conclusive
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	99.8736	1095	1204	95	conclusive
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	81.7614	561	1204	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	81.5688	532	1204	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.9192	500	1204	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	80.502	458	1204	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.4805	390	1204	95	below_threshold
Acinetobacter guillouiae	strain=CIP 63.46	GCA_000368145.1	106649	106649	type	True	80.0634	479	1204	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.9609	440	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:11,503] [INFO] DFAST Taxonomy check result was written to GCF_016027055.1_ASM1602705v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:11,504] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:11,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:11,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/checkm_data
[2024-01-25 19:37:11,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:11,541] [INFO] Task started: CheckM
[2024-01-25 19:37:11,541] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027055.1_ASM1602705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027055.1_ASM1602705v1_genomic.fna/checkm_input GCF_016027055.1_ASM1602705v1_genomic.fna/checkm_result
[2024-01-25 19:37:39,019] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:39,020] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:39,036] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:39,036] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:39,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027055.1_ASM1602705v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:39,037] [INFO] Task started: Blastn
[2024-01-25 19:37:39,037] [INFO] Running command: blastn -query GCF_016027055.1_ASM1602705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1f88acb-2a06-4f33-9846-0fbdbf4d6ab5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027055.1_ASM1602705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:39,936] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:39,938] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:39,938] [INFO] Target genome list was writen to GCF_016027055.1_ASM1602705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:39,946] [INFO] Task started: fastANI
[2024-01-25 19:37:39,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgb162d319-aaaf-45ee-bdec-3e08ef46745a/GCF_016027055.1_ASM1602705v1_genomic.fna.gz --refList GCF_016027055.1_ASM1602705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027055.1_ASM1602705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:55,093] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:55,105] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:55,105] [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_000368045.1	s__Acinetobacter johnsonii	99.972	1188	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	conclusive
GCF_002165305.2	s__Acinetobacter sp002165305	93.0204	974	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135205.1	s__Acinetobacter sp002135205	89.4875	936	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCF_004331175.1	s__Acinetobacter sp004331175	82.1856	538	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331255.1	s__Acinetobacter sp004331255	81.9841	546	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400735.1	s__Acinetobacter tandoii	81.7799	561	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_016599715.1	s__Acinetobacter sp002135245	81.7723	544	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_003024525.3	s__Acinetobacter cumulans	81.4605	530	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_004336635.1	s__Acinetobacter sp004336635	81.1203	574	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_003664645.1	s__Acinetobacter chengduensis	80.9237	499	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.8335	557	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.7886	556	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.6979	528	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135335.1	s__Acinetobacter sp002135335	80.5637	549	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711395.1	s__Acinetobacter sp003711395	80.5342	417	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.4663	504	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
GCF_001307195.1	s__Acinetobacter equi	80.3722	412	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368145.1	s__Acinetobacter guillouiae	80.0682	478	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
GCA_009912575.1	s__Acinetobacter bereziniae_A	79.6762	406	1204	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:55,106] [INFO] GTDB search result was written to GCF_016027055.1_ASM1602705v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:55,107] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:55,110] [INFO] DFAST_QC result json was written to GCF_016027055.1_ASM1602705v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:55,110] [INFO] DFAST_QC completed!
[2024-01-25 19:37:55,110] [INFO] Total running time: 0h1m4s