[2024-01-24 13:40:32,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:32,660] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:32,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference
[2024-01-24 13:40:34,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,041] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,041] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cbc6a3a-820b-4549-bad7-667173284e3e/GCF_001468035.1_ASM146803v1_genomic.fna.gz | prodigal -d GCF_001468035.1_ASM146803v1_genomic.fna/cds.fna -a GCF_001468035.1_ASM146803v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,449] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,450] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,450] [INFO] Running command: hmmsearch --tblout GCF_001468035.1_ASM146803v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/reference_markers.hmm GCF_001468035.1_ASM146803v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,754] [INFO] Found 6/6 markers.
[2024-01-24 13:40:41,784] [INFO] Query marker FASTA was written to GCF_001468035.1_ASM146803v1_genomic.fna/markers.fasta
[2024-01-24 13:40:41,785] [INFO] Task started: Blastn
[2024-01-24 13:40:41,785] [INFO] Running command: blastn -query GCF_001468035.1_ASM146803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/reference_markers.fasta -out GCF_001468035.1_ASM146803v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,439] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,442] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:42,443] [INFO] Target genome list was writen to GCF_001468035.1_ASM146803v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,451] [INFO] Task started: fastANI
[2024-01-24 13:40:42,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbc6a3a-820b-4549-bad7-667173284e3e/GCF_001468035.1_ASM146803v1_genomic.fna.gz --refList GCF_001468035.1_ASM146803v1_genomic.fna/target_genomes.txt --output GCF_001468035.1_ASM146803v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:50,911] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:50,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:50,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:50,921] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:50,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:50,922] [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
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	100.0	1114	1114	95	conclusive
Legionella tucsonensis	strain=1087-AZ-H	GCA_900640035.1	40335	40335	type	True	99.9839	1109	1114	95	conclusive
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	89.4078	930	1114	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_900639785.1	28082	28082	type	True	89.3849	894	1114	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_900640135.1	447	447	type	True	89.3399	918	1114	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	89.3341	926	1114	95	below_threshold
Legionella anisa	strain=FDAARGOS_1480	GCA_019930885.1	28082	28082	type	True	89.326	935	1114	95	below_threshold
Legionella bozemanae	strain=ATCC 33217	GCA_001648595.1	447	447	type	True	89.2898	929	1114	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	78.1398	176	1114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:50,924] [INFO] DFAST Taxonomy check result was written to GCF_001468035.1_ASM146803v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:50,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:50,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:50,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/checkm_data
[2024-01-24 13:40:50,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:50,963] [INFO] Task started: CheckM
[2024-01-24 13:40:50,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001468035.1_ASM146803v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001468035.1_ASM146803v1_genomic.fna/checkm_input GCF_001468035.1_ASM146803v1_genomic.fna/checkm_result
[2024-01-24 13:41:19,704] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:19,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:19,723] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:19,723] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:19,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001468035.1_ASM146803v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:19,724] [INFO] Task started: Blastn
[2024-01-24 13:41:19,724] [INFO] Running command: blastn -query GCF_001468035.1_ASM146803v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa95d144-7c05-49d0-b3a4-1ced0fea8ef3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001468035.1_ASM146803v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:20,862] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:20,865] [INFO] Selected 5 target genomes.
[2024-01-24 13:41:20,865] [INFO] Target genome list was writen to GCF_001468035.1_ASM146803v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:21,117] [INFO] Task started: fastANI
[2024-01-24 13:41:21,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cbc6a3a-820b-4549-bad7-667173284e3e/GCF_001468035.1_ASM146803v1_genomic.fna.gz --refList GCF_001468035.1_ASM146803v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001468035.1_ASM146803v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:26,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:26,580] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:26,581] [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_001468035.1	s__Legionella tucsonensis	100.0	1114	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001467525.1	s__Legionella anisa	89.4078	930	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_001648595.1	s__Legionella bozemanae	89.2898	929	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_014109805.1	s__Legionella sp014109805	89.0201	973	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467945.1	s__Legionella parisiensis	87.9163	965	1114	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:26,586] [INFO] GTDB search result was written to GCF_001468035.1_ASM146803v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:26,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:26,596] [INFO] DFAST_QC result json was written to GCF_001468035.1_ASM146803v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:26,597] [INFO] DFAST_QC completed!
[2024-01-24 13:41:26,597] [INFO] Total running time: 0h0m54s