[2024-01-24 14:38:48,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,543] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference
[2024-01-24 14:38:50,445] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,447] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,447] [INFO] Running command: gunzip -c /var/lib/cwl/stg80da3331-c8a1-43d6-b4d1-c14d3c281dea/GCF_018123985.1_PDT001010899.1_genomic.fna.gz | prodigal -d GCF_018123985.1_PDT001010899.1_genomic.fna/cds.fna -a GCF_018123985.1_PDT001010899.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:58,985] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:58,986] [INFO] Task started: HMMsearch
[2024-01-24 14:38:58,986] [INFO] Running command: hmmsearch --tblout GCF_018123985.1_PDT001010899.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/reference_markers.hmm GCF_018123985.1_PDT001010899.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:59,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:59,363] [INFO] Found 6/6 markers.
[2024-01-24 14:38:59,402] [INFO] Query marker FASTA was written to GCF_018123985.1_PDT001010899.1_genomic.fna/markers.fasta
[2024-01-24 14:38:59,403] [INFO] Task started: Blastn
[2024-01-24 14:38:59,403] [INFO] Running command: blastn -query GCF_018123985.1_PDT001010899.1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/reference_markers.fasta -out GCF_018123985.1_PDT001010899.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:00,137] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:00,141] [INFO] Selected 8 target genomes.
[2024-01-24 14:39:00,142] [INFO] Target genome list was writen to GCF_018123985.1_PDT001010899.1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:00,151] [INFO] Task started: fastANI
[2024-01-24 14:39:00,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg80da3331-c8a1-43d6-b4d1-c14d3c281dea/GCF_018123985.1_PDT001010899.1_genomic.fna.gz --refList GCF_018123985.1_PDT001010899.1_genomic.fna/target_genomes.txt --output GCF_018123985.1_PDT001010899.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:07,243] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:07,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:07,245] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:07,258] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:39:07,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:07,258] [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 baumannii	strain=ATCC 19606	GCA_014116795.1	470	470	type	True	98.0205	1078	1260	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_000737145.1	470	470	type	True	98.0087	1090	1260	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_009035845.1	470	470	type	True	97.9996	1082	1260	95	conclusive
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	97.981	1086	1260	95	conclusive
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	97.97	1090	1260	95	conclusive
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	89.1787	959	1260	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	80.1415	458	1260	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	78.6691	264	1260	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:07,262] [INFO] DFAST Taxonomy check result was written to GCF_018123985.1_PDT001010899.1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:07,263] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:07,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:07,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/checkm_data
[2024-01-24 14:39:07,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:07,316] [INFO] Task started: CheckM
[2024-01-24 14:39:07,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018123985.1_PDT001010899.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018123985.1_PDT001010899.1_genomic.fna/checkm_input GCF_018123985.1_PDT001010899.1_genomic.fna/checkm_result
[2024-01-24 14:39:39,933] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:39,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,953] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:39,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:39,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018123985.1_PDT001010899.1_genomic.fna/markers.fasta)
[2024-01-24 14:39:39,954] [INFO] Task started: Blastn
[2024-01-24 14:39:39,954] [INFO] Running command: blastn -query GCF_018123985.1_PDT001010899.1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a9e60a-d16a-4902-b180-85e9893f411f/dqc_reference/reference_markers_gtdb.fasta -out GCF_018123985.1_PDT001010899.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:41,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:41,063] [INFO] Selected 11 target genomes.
[2024-01-24 14:39:41,063] [INFO] Target genome list was writen to GCF_018123985.1_PDT001010899.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:41,071] [INFO] Task started: fastANI
[2024-01-24 14:39:41,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg80da3331-c8a1-43d6-b4d1-c14d3c281dea/GCF_018123985.1_PDT001010899.1_genomic.fna.gz --refList GCF_018123985.1_PDT001010899.1_genomic.fna/target_genomes_gtdb.txt --output GCF_018123985.1_PDT001010899.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:51,576] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:51,593] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:51,593] [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_009759685.1	s__Acinetobacter baumannii	97.9783	1091	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.86	96.67	0.89	0.80	5417	conclusive
GCF_000368085.1	s__Acinetobacter nosocomialis	92.104	1042	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.94	97.50	0.90	0.85	250	-
GCF_000368065.1	s__Acinetobacter seifertii	90.3757	998	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.88	96.48	0.87	0.81	81	-
GCF_002928115.1	s__Acinetobacter pittii_H	89.1425	1017	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.46	96.15	0.91	0.87	9	-
GCF_000369045.1	s__Acinetobacter pittii	89.0586	990	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.31	95.52	0.91	0.84	337	-
GCF_001605885.1	s__Acinetobacter lactucae	88.6815	984	1260	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	88.575	839	1260	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	88.4212	1016	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000313935.1	s__Acinetobacter sp000313935	87.987	992	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.37	99.37	0.94	0.94	2	-
GCF_000399665.1	s__Acinetobacter calcoaceticus_B	87.6977	981	1260	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016508255.1	s__Acinetobacter calcoaceticus_E	87.3873	955	1260	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 14:39:51,595] [INFO] GTDB search result was written to GCF_018123985.1_PDT001010899.1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:51,596] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:51,600] [INFO] DFAST_QC result json was written to GCF_018123985.1_PDT001010899.1_genomic.fna/dqc_result.json
[2024-01-24 14:39:51,600] [INFO] DFAST_QC completed!
[2024-01-24 14:39:51,600] [INFO] Total running time: 0h1m3s