[2024-01-24 11:36:20,740] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,742] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,743] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference
[2024-01-24 11:36:21,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:21,951] [INFO] Task started: Prodigal
[2024-01-24 11:36:21,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg9af6989b-d009-4996-a80d-baebd223c00f/GCF_001485025.1_ASM148502v1_genomic.fna.gz | prodigal -d GCF_001485025.1_ASM148502v1_genomic.fna/cds.fna -a GCF_001485025.1_ASM148502v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:30,347] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:30,348] [INFO] Task started: HMMsearch
[2024-01-24 11:36:30,348] [INFO] Running command: hmmsearch --tblout GCF_001485025.1_ASM148502v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/reference_markers.hmm GCF_001485025.1_ASM148502v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:30,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:30,628] [INFO] Found 6/6 markers.
[2024-01-24 11:36:30,671] [INFO] Query marker FASTA was written to GCF_001485025.1_ASM148502v1_genomic.fna/markers.fasta
[2024-01-24 11:36:30,672] [INFO] Task started: Blastn
[2024-01-24 11:36:30,672] [INFO] Running command: blastn -query GCF_001485025.1_ASM148502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/reference_markers.fasta -out GCF_001485025.1_ASM148502v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:31,419] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:31,423] [INFO] Selected 18 target genomes.
[2024-01-24 11:36:31,424] [INFO] Target genome list was writen to GCF_001485025.1_ASM148502v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:31,513] [INFO] Task started: fastANI
[2024-01-24 11:36:31,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af6989b-d009-4996-a80d-baebd223c00f/GCF_001485025.1_ASM148502v1_genomic.fna.gz --refList GCF_001485025.1_ASM148502v1_genomic.fna/target_genomes.txt --output GCF_001485025.1_ASM148502v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:43,003] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:43,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:43,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:43,029] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:36:43,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:43,030] [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 bouvetii	strain=DSM 14964	GCA_000373725.1	202951	202951	type	True	99.9957	1103	1104	95	conclusive
Acinetobacter bouvetii	strain=CIP 107468	GCA_000368865.1	202951	202951	type	True	99.9905	1103	1104	95	conclusive
Acinetobacter pragensis	strain=ANC 4149	GCA_001605895.1	1806892	1806892	type	True	85.5222	861	1104	95	below_threshold
Acinetobacter tianfuensis	strain=WCHAc060012	GCA_003611465.1	2419603	2419603	type	True	81.625	627	1104	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	81.4296	590	1104	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	81.1521	480	1104	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	81.071	468	1104	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	80.9441	490	1104	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	80.7484	555	1104	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.6267	549	1104	95	below_threshold
Acinetobacter gandensis	strain=ANC 4275	GCA_001678755.1	1443941	1443941	type	True	80.5362	497	1104	95	below_threshold
Acinetobacter pseudolwoffii	strain=ANC 5044	GCA_002803605.1	2053287	2053287	type	True	80.1193	450	1104	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.9859	447	1104	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.9537	453	1104	95	below_threshold
Acinetobacter indicus	strain=CIP 110367	GCA_000488255.1	756892	756892	type	True	79.8612	470	1104	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.4273	356	1104	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	78.5488	273	1104	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.2632	299	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:43,031] [INFO] DFAST Taxonomy check result was written to GCF_001485025.1_ASM148502v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:43,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:43,032] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:43,032] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/checkm_data
[2024-01-24 11:36:43,033] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:43,070] [INFO] Task started: CheckM
[2024-01-24 11:36:43,071] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001485025.1_ASM148502v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001485025.1_ASM148502v1_genomic.fna/checkm_input GCF_001485025.1_ASM148502v1_genomic.fna/checkm_result
[2024-01-24 11:37:13,727] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:13,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:13,749] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:13,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:13,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001485025.1_ASM148502v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:13,750] [INFO] Task started: Blastn
[2024-01-24 11:37:13,750] [INFO] Running command: blastn -query GCF_001485025.1_ASM148502v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e4e7381-49ec-49fd-aa47-1bbfafca74b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001485025.1_ASM148502v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:14,988] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:14,993] [INFO] Selected 12 target genomes.
[2024-01-24 11:37:14,993] [INFO] Target genome list was writen to GCF_001485025.1_ASM148502v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:15,015] [INFO] Task started: fastANI
[2024-01-24 11:37:15,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg9af6989b-d009-4996-a80d-baebd223c00f/GCF_001485025.1_ASM148502v1_genomic.fna.gz --refList GCF_001485025.1_ASM148502v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001485025.1_ASM148502v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:23,834] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:23,851] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:23,851] [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_000368865.1	s__Acinetobacter bouvetii	99.9905	1103	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.30	95.72	0.97	0.92	6	conclusive
GCF_001605895.1	s__Acinetobacter pragensis	85.5222	861	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135435.1	s__Acinetobacter sp002135435	84.147	844	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696615.3	s__Acinetobacter sp001696615	82.0371	728	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611465.1	s__Acinetobacter tianfuensis	81.6276	626	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135295.1	s__Acinetobacter sp002135295	80.8497	572	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.7192	553	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_003664645.1	s__Acinetobacter chengduensis	80.631	549	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_900096895.1	s__Acinetobacter kookii	80.4207	540	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.51	0.92	0.92	2	-
GCF_002135355.1	s__Acinetobacter sp002135355	80.3319	553	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803605.1	s__Acinetobacter pseudolwoffii	80.1067	451	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.62	97.19	0.89	0.84	25	-
GCF_004331285.1	s__Acinetobacter sp004331285	79.756	499	1104	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:23,853] [INFO] GTDB search result was written to GCF_001485025.1_ASM148502v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:23,853] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:23,857] [INFO] DFAST_QC result json was written to GCF_001485025.1_ASM148502v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:23,857] [INFO] DFAST_QC completed!
[2024-01-24 11:37:23,857] [INFO] Total running time: 0h1m3s