[2024-01-25 19:10:35,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:35,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:35,603] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference
[2024-01-25 19:10:36,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:36,828] [INFO] Task started: Prodigal
[2024-01-25 19:10:36,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg613626c5-7268-4b20-8990-060b116990ef/GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna.gz | prodigal -d GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/cds.fna -a GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:44,439] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:44,439] [INFO] Task started: HMMsearch
[2024-01-25 19:10:44,439] [INFO] Running command: hmmsearch --tblout GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/reference_markers.hmm GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:44,736] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:44,737] [INFO] Found 6/6 markers.
[2024-01-25 19:10:44,764] [INFO] Query marker FASTA was written to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/markers.fasta
[2024-01-25 19:10:44,765] [INFO] Task started: Blastn
[2024-01-25 19:10:44,765] [INFO] Running command: blastn -query GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/reference_markers.fasta -out GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:45,415] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:45,418] [INFO] Selected 20 target genomes.
[2024-01-25 19:10:45,418] [INFO] Target genome list was writen to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:45,429] [INFO] Task started: fastANI
[2024-01-25 19:10:45,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg613626c5-7268-4b20-8990-060b116990ef/GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna.gz --refList GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/target_genomes.txt --output GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:58,368] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:58,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:58,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:58,381] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:58,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:58,381] [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 soli	strain=KCTC 22184	GCA_000760595.1	487316	487316	type	True	99.9865	1090	1116	95	conclusive
Acinetobacter baylyi	strain=CIP 107474	GCA_000368685.1	202950	202950	type	True	83.2548	711	1116	95	below_threshold
Acinetobacter baylyi	strain=DSM 14961	GCA_000621045.1	202950	202950	type	True	83.0825	704	1116	95	below_threshold
Acinetobacter ursingii	strain=CIP 107286	GCA_000368825.1	108980	108980	type	True	80.0095	452	1116	95	below_threshold
Acinetobacter ursingii	strain=FDAARGOS_1095	GCA_016726205.1	108980	108980	type	True	79.9973	472	1116	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	79.9282	329	1116	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	79.8137	468	1116	95	below_threshold
Acinetobacter septicus	strain=FDAARGOS_1401	GCA_019355975.1	465797	465797	type	True	79.7283	489	1116	95	below_threshold
Acinetobacter guerrae	strain=AC 1271	GCA_009372255.1	1843371	1843371	type	True	79.7243	459	1116	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.4278	300	1116	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	79.369	335	1116	95	below_threshold
Acinetobacter gerneri	strain=CIP 107464	GCA_000368565.1	202952	202952	type	True	79.1019	303	1116	95	below_threshold
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	78.9751	359	1116	95	below_threshold
Acinetobacter stercoris	strain=KPC-SM-21	GCA_900323515.1	2126983	2126983	type	True	78.8738	249	1116	95	below_threshold
Acinetobacter gerneri	strain=MTCC 9824	GCA_000430245.1	202952	202952	type	True	78.7799	294	1116	95	below_threshold
Acinetobacter gerneri	strain=KCTC 12415	GCA_000747725.1	202952	202952	type	True	78.7283	286	1116	95	below_threshold
Acinetobacter halotolerans	strain=JCM 31009	GCA_004208515.1	1752076	1752076	type	True	78.7133	327	1116	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	78.6939	294	1116	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	78.5662	286	1116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:58,382] [INFO] DFAST Taxonomy check result was written to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:58,383] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:58,383] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:58,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/checkm_data
[2024-01-25 19:10:58,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:58,419] [INFO] Task started: CheckM
[2024-01-25 19:10:58,419] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/checkm_input GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/checkm_result
[2024-01-25 19:11:26,050] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:26,051] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:26,068] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:26,069] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:26,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/markers.fasta)
[2024-01-25 19:11:26,069] [INFO] Task started: Blastn
[2024-01-25 19:11:26,069] [INFO] Running command: blastn -query GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8f3b7a3-6843-44db-8957-7ff084a789d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:27,139] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:27,142] [INFO] Selected 20 target genomes.
[2024-01-25 19:11:27,142] [INFO] Target genome list was writen to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:27,157] [INFO] Task started: fastANI
[2024-01-25 19:11:27,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg613626c5-7268-4b20-8990-060b116990ef/GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna.gz --refList GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/target_genomes_gtdb.txt --output GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:40,946] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:40,957] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:40,958] [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_000760595.1	s__Acinetobacter soli	99.9865	1090	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.45	98.17	0.92	0.88	38	conclusive
GCF_000368685.1	s__Acinetobacter baylyi	83.3013	709	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.85	98.65	0.98	0.93	13	-
GCF_000368825.1	s__Acinetobacter ursingii	80.002	452	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.69	96.95	0.88	0.80	69	-
GCF_900625095.1	s__Acinetobacter sp900625095	79.8251	467	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009372255.1	s__Acinetobacter guerrae	79.7243	459	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.44	98.41	0.90	0.89	3	-
GCF_016624945.1	s__Acinetobacter sp016624945	79.4759	442	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.57	99.14	0.97	0.94	3	-
GCF_000368585.1	s__Acinetobacter venetianus	79.3987	338	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_000369505.1	s__Acinetobacter sp000369505	79.2824	332	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.55	96.55	0.85	0.85	2	-
GCF_000400715.1	s__Acinetobacter sp000400715	79.2707	357	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009884975.1	s__Acinetobacter dispersus	79.2453	346	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369525.1	s__Acinetobacter sp000369525	79.1368	365	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	78.976	319	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635885.1	s__Acinetobacter vivianii	78.9751	359	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_900323515.1	s__Acinetobacter stercoris	78.8545	250	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.59	98.59	0.92	0.92	2	-
GCF_004331255.1	s__Acinetobacter sp004331255	78.8064	362	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331035.1	s__Acinetobacter sp004331035	78.7974	357	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004208515.1	s__Acinetobacter halotolerans	78.7133	327	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.44	95.44	0.89	0.89	2	-
GCA_003987695.1	s__Acinetobacter sp003987695	78.6458	304	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.01	98.01	0.75	0.75	2	-
GCF_001678755.1	s__Acinetobacter gandensis	78.566	286	1116	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.74	98.30	0.89	0.84	6	-
GCF_002233755.1	s__Acinetobacter piscicola	78.52	293	1116	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 19:11:40,959] [INFO] GTDB search result was written to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:40,960] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:40,964] [INFO] DFAST_QC result json was written to GCF_000368705.1_Acin_soli_CIP_110264_V1_genomic.fna/dqc_result.json
[2024-01-25 19:11:40,964] [INFO] DFAST_QC completed!
[2024-01-25 19:11:40,964] [INFO] Total running time: 0h1m5s