[2024-01-24 15:10:20,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,167] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference
[2024-01-24 15:10:22,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,722] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,723] [INFO] Running command: gunzip -c /var/lib/cwl/stged335f74-134d-49ab-bbb9-5d9ec07d6e05/GCF_013004375.1_ASM1300437v1_genomic.fna.gz | prodigal -d GCF_013004375.1_ASM1300437v1_genomic.fna/cds.fna -a GCF_013004375.1_ASM1300437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:30,307] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:30,308] [INFO] Task started: HMMsearch
[2024-01-24 15:10:30,308] [INFO] Running command: hmmsearch --tblout GCF_013004375.1_ASM1300437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/reference_markers.hmm GCF_013004375.1_ASM1300437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:30,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:30,570] [INFO] Found 6/6 markers.
[2024-01-24 15:10:30,598] [INFO] Query marker FASTA was written to GCF_013004375.1_ASM1300437v1_genomic.fna/markers.fasta
[2024-01-24 15:10:30,598] [INFO] Task started: Blastn
[2024-01-24 15:10:30,599] [INFO] Running command: blastn -query GCF_013004375.1_ASM1300437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/reference_markers.fasta -out GCF_013004375.1_ASM1300437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:31,319] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:31,323] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:31,323] [INFO] Target genome list was writen to GCF_013004375.1_ASM1300437v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:31,355] [INFO] Task started: fastANI
[2024-01-24 15:10:31,355] [INFO] Running command: fastANI --query /var/lib/cwl/stged335f74-134d-49ab-bbb9-5d9ec07d6e05/GCF_013004375.1_ASM1300437v1_genomic.fna.gz --refList GCF_013004375.1_ASM1300437v1_genomic.fna/target_genomes.txt --output GCF_013004375.1_ASM1300437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:42,107] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:42,108] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:42,108] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:42,127] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:42,127] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:42,128] [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 terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	100.0	1067	1069	95	conclusive
Acinetobacter terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	91.2525	900	1069	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	84.8561	786	1069	95	below_threshold
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	82.2558	638	1069	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	81.6087	631	1069	95	below_threshold
Acinetobacter lwoffii	strain=FDAARGOS 1393	GCA_019048305.1	28090	28090	type	True	80.8222	552	1069	95	below_threshold
Acinetobacter lwoffii	strain=NCTC5866	GCA_900699155.1	28090	28090	type	True	80.7854	554	1069	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.7562	571	1069	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.6366	479	1069	95	below_threshold
Acinetobacter gandensis	strain=CCUG 68482	GCA_008802205.1	1443941	1443941	type	True	80.602	536	1069	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	80.5588	516	1069	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.5587	542	1069	95	below_threshold
Acinetobacter wuhouensis	strain=WCHA60	GCA_001696605.3	1879050	1879050	type	True	80.2619	493	1069	95	below_threshold
Acinetobacter sichuanensis	strain=WCHAc060041	GCA_003024515.2	2136183	2136183	type	True	79.9482	478	1069	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.2903	356	1069	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.7824	398	1069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:42,130] [INFO] DFAST Taxonomy check result was written to GCF_013004375.1_ASM1300437v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:42,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:42,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:42,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/checkm_data
[2024-01-24 15:10:42,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:42,172] [INFO] Task started: CheckM
[2024-01-24 15:10:42,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013004375.1_ASM1300437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013004375.1_ASM1300437v1_genomic.fna/checkm_input GCF_013004375.1_ASM1300437v1_genomic.fna/checkm_result
[2024-01-24 15:11:13,301] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:13,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,322] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:13,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:13,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013004375.1_ASM1300437v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:13,324] [INFO] Task started: Blastn
[2024-01-24 15:11:13,324] [INFO] Running command: blastn -query GCF_013004375.1_ASM1300437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c67256e-53c8-42ff-87d7-47891f2f40de/dqc_reference/reference_markers_gtdb.fasta -out GCF_013004375.1_ASM1300437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:14,509] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:14,513] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:14,513] [INFO] Target genome list was writen to GCF_013004375.1_ASM1300437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:14,520] [INFO] Task started: fastANI
[2024-01-24 15:11:14,520] [INFO] Running command: fastANI --query /var/lib/cwl/stged335f74-134d-49ab-bbb9-5d9ec07d6e05/GCF_013004375.1_ASM1300437v1_genomic.fna.gz --refList GCF_013004375.1_ASM1300437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013004375.1_ASM1300437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:20,600] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:20,608] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:20,609] [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_013004375.1	s__Acinetobacter terrae	100.0	1067	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	conclusive
GCF_004336635.1	s__Acinetobacter sp004336635	92.5833	894	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_004331155.1	s__Acinetobacter terrestris	91.2525	900	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCF_001647545.1	s__Acinetobacter sp001647545	89.4443	846	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_004331285.1	s__Acinetobacter sp004331285	89.1752	870	1069	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	84.8205	745	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014769185.1	s__Acinetobacter lwoffii_D	80.9745	541	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2371	96.35	96.24	0.87	0.85	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:20,611] [INFO] GTDB search result was written to GCF_013004375.1_ASM1300437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:20,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:20,616] [INFO] DFAST_QC result json was written to GCF_013004375.1_ASM1300437v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:20,616] [INFO] DFAST_QC completed!
[2024-01-24 15:11:20,616] [INFO] Total running time: 0h1m0s