[2024-01-24 10:58:06,468] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference
[2024-01-24 10:58:09,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,635] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,636] [INFO] Running command: gunzip -c /var/lib/cwl/stg9deb32d9-8e25-4f74-8067-dba25ca81582/GCF_024390955.1_ASM2439095v1_genomic.fna.gz | prodigal -d GCF_024390955.1_ASM2439095v1_genomic.fna/cds.fna -a GCF_024390955.1_ASM2439095v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:17,678] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:17,678] [INFO] Task started: HMMsearch
[2024-01-24 10:58:17,679] [INFO] Running command: hmmsearch --tblout GCF_024390955.1_ASM2439095v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/reference_markers.hmm GCF_024390955.1_ASM2439095v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:18,026] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:18,027] [INFO] Found 6/6 markers.
[2024-01-24 10:58:18,068] [INFO] Query marker FASTA was written to GCF_024390955.1_ASM2439095v1_genomic.fna/markers.fasta
[2024-01-24 10:58:18,069] [INFO] Task started: Blastn
[2024-01-24 10:58:18,069] [INFO] Running command: blastn -query GCF_024390955.1_ASM2439095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/reference_markers.fasta -out GCF_024390955.1_ASM2439095v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:18,717] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:18,721] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:18,722] [INFO] Target genome list was writen to GCF_024390955.1_ASM2439095v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:18,747] [INFO] Task started: fastANI
[2024-01-24 10:58:18,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg9deb32d9-8e25-4f74-8067-dba25ca81582/GCF_024390955.1_ASM2439095v1_genomic.fna.gz --refList GCF_024390955.1_ASM2439095v1_genomic.fna/target_genomes.txt --output GCF_024390955.1_ASM2439095v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:27,371] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:27,371] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:27,372] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:27,380] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:58:27,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:27,381] [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 pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	100.0	1291	1293	95	conclusive
Acinetobacter pittii	strain=CIP 70.29	GCA_000369045.1	48296	48296	type	True	97.1721	1123	1293	95	conclusive
Acinetobacter pittii	strain=FDAARGOS 1399	GCA_019047205.1	48296	48296	type	True	97.067	1160	1293	95	conclusive
Acinetobacter pittii	strain=DSM 25618	GCA_000836015.1	48296	48296	type	True	97.0616	1155	1293	95	conclusive
Acinetobacter lactucae	strain=NRRL B-41902	GCA_001605885.1	1785128	1785128	type	True	93.4761	1077	1293	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	89.1683	1056	1293	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	89.1367	1065	1293	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.529	491	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:27,383] [INFO] DFAST Taxonomy check result was written to GCF_024390955.1_ASM2439095v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:27,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:27,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:27,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/checkm_data
[2024-01-24 10:58:27,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:27,427] [INFO] Task started: CheckM
[2024-01-24 10:58:27,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024390955.1_ASM2439095v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024390955.1_ASM2439095v1_genomic.fna/checkm_input GCF_024390955.1_ASM2439095v1_genomic.fna/checkm_result
[2024-01-24 10:58:58,338] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:58,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:58,366] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:58,366] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:58,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024390955.1_ASM2439095v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:58,368] [INFO] Task started: Blastn
[2024-01-24 10:58:58,368] [INFO] Running command: blastn -query GCF_024390955.1_ASM2439095v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8375f0d-1b3d-40a7-a7f5-da607d19ed4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_024390955.1_ASM2439095v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:59,239] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:59,245] [INFO] Selected 11 target genomes.
[2024-01-24 10:58:59,245] [INFO] Target genome list was writen to GCF_024390955.1_ASM2439095v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:59,255] [INFO] Task started: fastANI
[2024-01-24 10:58:59,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg9deb32d9-8e25-4f74-8067-dba25ca81582/GCF_024390955.1_ASM2439095v1_genomic.fna.gz --refList GCF_024390955.1_ASM2439095v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024390955.1_ASM2439095v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:07,766] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:07,778] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 10:59:07,779] [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_000369045.1	s__Acinetobacter pittii	97.1721	1123	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	inconclusive
GCF_013009345.1	s__Acinetobacter sp013009345	95.1265	1100	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.73	96.63	0.87	0.86	5	inconclusive
GCF_002928115.1	s__Acinetobacter pittii_H	94.5271	1068	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_001605885.1	s__Acinetobacter lactucae	93.4937	1076	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.34	96.55	0.91	0.85	16	-
GCF_013344765.1	s__Acinetobacter lactucae_A	93.0858	898	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.51	97.14	0.90	0.87	4	-
GCF_000399685.1	s__Acinetobacter pittii_E	92.5489	1035	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368765.1	s__Acinetobacter junii	80.5522	491	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.03	97.21	0.88	0.81	75	-
GCF_011058205.1	s__Acinetobacter fasciculus	79.7243	310	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	96.2485	96.87	96.57	0.87	0.83	19	-
GCA_002296655.1	s__Acinetobacter sp002296655	79.1894	310	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.93	0.93	2	-
GCF_009557235.1	s__Acinetobacter wanghuae	79.0103	325	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.95	99.95	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,780] [INFO] GTDB search result was written to GCF_024390955.1_ASM2439095v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:07,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:07,785] [INFO] DFAST_QC result json was written to GCF_024390955.1_ASM2439095v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:07,786] [INFO] DFAST_QC completed!
[2024-01-24 10:59:07,786] [INFO] Total running time: 0h1m1s