[2024-01-24 13:46:40,627] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference
[2024-01-24 13:46:42,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:42,030] [INFO] Task started: Prodigal
[2024-01-24 13:46:42,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg00104fbd-8614-4697-998f-208b6fe39e98/GCF_009372255.1_ASM937225v1_genomic.fna.gz | prodigal -d GCF_009372255.1_ASM937225v1_genomic.fna/cds.fna -a GCF_009372255.1_ASM937225v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:50,118] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:50,118] [INFO] Task started: HMMsearch
[2024-01-24 13:46:50,119] [INFO] Running command: hmmsearch --tblout GCF_009372255.1_ASM937225v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/reference_markers.hmm GCF_009372255.1_ASM937225v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:50,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:50,384] [INFO] Found 6/6 markers.
[2024-01-24 13:46:50,418] [INFO] Query marker FASTA was written to GCF_009372255.1_ASM937225v1_genomic.fna/markers.fasta
[2024-01-24 13:46:50,418] [INFO] Task started: Blastn
[2024-01-24 13:46:50,419] [INFO] Running command: blastn -query GCF_009372255.1_ASM937225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/reference_markers.fasta -out GCF_009372255.1_ASM937225v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:51,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:51,130] [INFO] Selected 12 target genomes.
[2024-01-24 13:46:51,131] [INFO] Target genome list was writen to GCF_009372255.1_ASM937225v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:51,137] [INFO] Task started: fastANI
[2024-01-24 13:46:51,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg00104fbd-8614-4697-998f-208b6fe39e98/GCF_009372255.1_ASM937225v1_genomic.fna.gz --refList GCF_009372255.1_ASM937225v1_genomic.fna/target_genomes.txt --output GCF_009372255.1_ASM937225v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:00,543] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:00,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:00,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:00,554] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:00,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:00,554] [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 guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	100.0	1121	1122	95	conclusive
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	88.5722	905	1122	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	88.5231	893	1122	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	88.4899	902	1122	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	83.8364	810	1122	95	below_threshold
Acinetobacter oleivorans	strain=KCTC 23045	GCA_000836035.1	1148157	1148157	suspected-type	True	79.2366	428	1122	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	78.747	356	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:00,556] [INFO] DFAST Taxonomy check result was written to GCF_009372255.1_ASM937225v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:00,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:00,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:00,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/checkm_data
[2024-01-24 13:47:00,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:00,594] [INFO] Task started: CheckM
[2024-01-24 13:47:00,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009372255.1_ASM937225v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009372255.1_ASM937225v1_genomic.fna/checkm_input GCF_009372255.1_ASM937225v1_genomic.fna/checkm_result
[2024-01-24 13:47:29,972] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:29,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:29,991] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:29,992] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:29,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009372255.1_ASM937225v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:29,993] [INFO] Task started: Blastn
[2024-01-24 13:47:29,993] [INFO] Running command: blastn -query GCF_009372255.1_ASM937225v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a033c57-0aba-442e-9054-8c7d95df3c53/dqc_reference/reference_markers_gtdb.fasta -out GCF_009372255.1_ASM937225v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:30,888] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:30,892] [INFO] Selected 19 target genomes.
[2024-01-24 13:47:30,893] [INFO] Target genome list was writen to GCF_009372255.1_ASM937225v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:30,939] [INFO] Task started: fastANI
[2024-01-24 13:47:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg00104fbd-8614-4697-998f-208b6fe39e98/GCF_009372255.1_ASM937225v1_genomic.fna.gz --refList GCF_009372255.1_ASM937225v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009372255.1_ASM937225v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:44,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:44,091] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:44,091] [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_009372255.1	s__Acinetobacter guerrae	100.0	1121	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	conclusive
GCF_000368825.1	s__Acinetobacter ursingii	88.5231	893	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
GCF_016624945.1	s__Acinetobacter sp016624945	85.7626	877	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_900625095.1	s__Acinetobacter sp900625095	83.8359	810	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368685.1	s__Acinetobacter baylyi	80.3255	519	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
GCF_002928115.1	s__Acinetobacter pittii_H	79.4515	423	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_009884975.1	s__Acinetobacter dispersus	79.4319	389	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000368065.1	s__Acinetobacter seifertii	79.3043	422	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_000196795.1	s__Acinetobacter oleivorans	79.2762	421	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.22	95.12	0.90	0.85	40	-
GCF_014635885.1	s__Acinetobacter vivianii	79.2325	427	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	79.0806	425	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214135.1	s__Acinetobacter sp000214135	78.968	391	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002296655.1	s__Acinetobacter sp002296655	78.8998	306	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
GCF_006757745.1	s__Acinetobacter radioresistens	78.8323	307	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.57	97.95	0.93	0.87	74	-
GCF_000368145.1	s__Acinetobacter guillouiae	78.7225	413	1122	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.78	96.36	0.91	0.85	14	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:44,093] [INFO] GTDB search result was written to GCF_009372255.1_ASM937225v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:44,093] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:44,099] [INFO] DFAST_QC result json was written to GCF_009372255.1_ASM937225v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:44,099] [INFO] DFAST_QC completed!
[2024-01-24 13:47:44,099] [INFO] Total running time: 0h1m3s