[2024-01-25 19:36:20,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:20,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:20,563] [INFO] DQC Reference Directory: /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference
[2024-01-25 19:36:21,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:21,704] [INFO] Task started: Prodigal
[2024-01-25 19:36:21,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg87c44d53-7890-4b21-af83-8d2a8870db35/GCF_003664645.1_ASM366464v1_genomic.fna.gz | prodigal -d GCF_003664645.1_ASM366464v1_genomic.fna/cds.fna -a GCF_003664645.1_ASM366464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:29,163] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:29,163] [INFO] Task started: HMMsearch
[2024-01-25 19:36:29,164] [INFO] Running command: hmmsearch --tblout GCF_003664645.1_ASM366464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/reference_markers.hmm GCF_003664645.1_ASM366464v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:29,383] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:29,384] [INFO] Found 6/6 markers.
[2024-01-25 19:36:29,415] [INFO] Query marker FASTA was written to GCF_003664645.1_ASM366464v1_genomic.fna/markers.fasta
[2024-01-25 19:36:29,416] [INFO] Task started: Blastn
[2024-01-25 19:36:29,416] [INFO] Running command: blastn -query GCF_003664645.1_ASM366464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/reference_markers.fasta -out GCF_003664645.1_ASM366464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:30,093] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:30,095] [INFO] Selected 17 target genomes.
[2024-01-25 19:36:30,095] [INFO] Target genome list was writen to GCF_003664645.1_ASM366464v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:30,100] [INFO] Task started: fastANI
[2024-01-25 19:36:30,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c44d53-7890-4b21-af83-8d2a8870db35/GCF_003664645.1_ASM366464v1_genomic.fna.gz --refList GCF_003664645.1_ASM366464v1_genomic.fna/target_genomes.txt --output GCF_003664645.1_ASM366464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:36:41,552] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:41,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:36:41,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:36:41,563] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:36:41,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:36:41,563] [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 chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	100.0	1213	1217	95	conclusive
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	88.7835	944	1217	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	82.1145	652	1217	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	81.6389	594	1217	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	81.5758	585	1217	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.9757	478	1217	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	80.8077	503	1217	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.7501	506	1217	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.7168	564	1217	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	80.5993	494	1217	95	below_threshold
Acinetobacter equi	strain=114	GCA_001307195.1	1324350	1324350	type	True	80.3718	443	1217	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.1504	432	1217	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	79.8586	389	1217	95	below_threshold
Acinetobacter piscicola	strain=LW15	GCA_002233755.1	2006115	2006115	type	True	79.7297	411	1217	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.507	411	1217	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.9444	361	1217	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.5823	330	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:36:41,565] [INFO] DFAST Taxonomy check result was written to GCF_003664645.1_ASM366464v1_genomic.fna/tc_result.tsv
[2024-01-25 19:36:41,565] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:36:41,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:36:41,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/checkm_data
[2024-01-25 19:36:41,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:36:41,605] [INFO] Task started: CheckM
[2024-01-25 19:36:41,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664645.1_ASM366464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664645.1_ASM366464v1_genomic.fna/checkm_input GCF_003664645.1_ASM366464v1_genomic.fna/checkm_result
[2024-01-25 19:37:08,742] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:08,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:08,788] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:08,788] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:08,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664645.1_ASM366464v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:08,788] [INFO] Task started: Blastn
[2024-01-25 19:37:08,789] [INFO] Running command: blastn -query GCF_003664645.1_ASM366464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54c665f1-8ad7-4013-bc7a-cf15b49d5c2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664645.1_ASM366464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:09,867] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:09,869] [INFO] Selected 15 target genomes.
[2024-01-25 19:37:09,869] [INFO] Target genome list was writen to GCF_003664645.1_ASM366464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:09,920] [INFO] Task started: fastANI
[2024-01-25 19:37:09,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg87c44d53-7890-4b21-af83-8d2a8870db35/GCF_003664645.1_ASM366464v1_genomic.fna.gz --refList GCF_003664645.1_ASM366464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664645.1_ASM366464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:20,878] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:20,890] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:37:20,890] [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_003664645.1	s__Acinetobacter chengduensis	100.0	1213	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	conclusive
GCF_003024525.3	s__Acinetobacter cumulans	88.7709	945	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	97.84	0.86	0.82	9	-
GCF_003611465.1	s__Acinetobacter tianfuensis	82.1149	652	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678755.1	s__Acinetobacter gandensis	81.6389	594	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_002018365.1	s__Acinetobacter sp002018365	81.4476	625	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_001647675.1	s__Acinetobacter sp001647675	81.2071	499	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372215.1	s__Acinetobacter portensis	81.0042	475	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.69	98.69	0.93	0.93	2	-
GCF_000368045.1	s__Acinetobacter johnsonii	80.7783	503	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_001707755.1	s__Acinetobacter celticus	80.7274	563	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002165305.2	s__Acinetobacter sp002165305	80.6672	505	1217	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	80.4947	447	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_002135355.1	s__Acinetobacter sp002135355	80.4906	515	1217	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	80.4526	497	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCF_002688565.1	s__Acinetobacter sp002688565	80.4402	462	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135315.1	s__Acinetobacter sp002135315	80.4038	513	1217	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 19:37:20,893] [INFO] GTDB search result was written to GCF_003664645.1_ASM366464v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:20,894] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:20,897] [INFO] DFAST_QC result json was written to GCF_003664645.1_ASM366464v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:20,898] [INFO] DFAST_QC completed!
[2024-01-25 19:37:20,898] [INFO] Total running time: 0h1m0s