[2024-01-24 14:30:30,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,056] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference
[2024-01-24 14:30:31,414] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,414] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,415] [INFO] Running command: gunzip -c /var/lib/cwl/stga45cf031-63dc-4cd6-bedc-5c9b1822d337/GCF_900637585.1_52067_F01_genomic.fna.gz | prodigal -d GCF_900637585.1_52067_F01_genomic.fna/cds.fna -a GCF_900637585.1_52067_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:39,262] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:39,263] [INFO] Task started: HMMsearch
[2024-01-24 14:30:39,263] [INFO] Running command: hmmsearch --tblout GCF_900637585.1_52067_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/reference_markers.hmm GCF_900637585.1_52067_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:39,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:39,499] [INFO] Found 6/6 markers.
[2024-01-24 14:30:39,530] [INFO] Query marker FASTA was written to GCF_900637585.1_52067_F01_genomic.fna/markers.fasta
[2024-01-24 14:30:39,531] [INFO] Task started: Blastn
[2024-01-24 14:30:39,531] [INFO] Running command: blastn -query GCF_900637585.1_52067_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/reference_markers.fasta -out GCF_900637585.1_52067_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:40,219] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:40,222] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:40,223] [INFO] Target genome list was writen to GCF_900637585.1_52067_F01_genomic.fna/target_genomes.txt
[2024-01-24 14:30:40,233] [INFO] Task started: fastANI
[2024-01-24 14:30:40,233] [INFO] Running command: fastANI --query /var/lib/cwl/stga45cf031-63dc-4cd6-bedc-5c9b1822d337/GCF_900637585.1_52067_F01_genomic.fna.gz --refList GCF_900637585.1_52067_F01_genomic.fna/target_genomes.txt --output GCF_900637585.1_52067_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:47,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:47,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:47,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:47,783] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:30:47,783] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:47,783] [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 pneumophila subsp. pascullei	strain=NCTC12273	GCA_900637585.1	91890	446	type	True	100.0	1151	1152	95	conclusive
Legionella pneumophila subsp. pascullei	strain=ATCC 33737	GCA_000586255.1	91890	446	type	True	99.9713	1141	1152	95	conclusive
Legionella pneumophila subsp. fraseri	strain=Los Angeles 1	GCA_900639965.1	91892	446	type	True	93.8543	1018	1152	95	below_threshold
Legionella pneumophila subsp. fraseri	strain=ATCC 33156	GCA_000586315.1	91892	446	type	True	93.8165	1014	1152	95	below_threshold
Legionella pneumophila	strain=NCTC11192	GCA_900452735.1	446	446	type	True	91.2766	1006	1152	95	below_threshold
Legionella pneumophila	strain=FDAARGOS_779	GCA_006364635.1	446	446	type	True	91.2739	1007	1152	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	91.2411	1003	1152	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	78.0722	145	1152	95	below_threshold
Legionella adelaidensis	strain=NCTC12735	GCA_900637865.1	45056	45056	type	True	77.5897	69	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:47,785] [INFO] DFAST Taxonomy check result was written to GCF_900637585.1_52067_F01_genomic.fna/tc_result.tsv
[2024-01-24 14:30:47,786] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:47,786] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:47,786] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/checkm_data
[2024-01-24 14:30:47,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:47,822] [INFO] Task started: CheckM
[2024-01-24 14:30:47,823] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637585.1_52067_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637585.1_52067_F01_genomic.fna/checkm_input GCF_900637585.1_52067_F01_genomic.fna/checkm_result
[2024-01-24 14:31:16,895] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:16,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:16,916] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:16,916] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:16,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637585.1_52067_F01_genomic.fna/markers.fasta)
[2024-01-24 14:31:16,917] [INFO] Task started: Blastn
[2024-01-24 14:31:16,917] [INFO] Running command: blastn -query GCF_900637585.1_52067_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb427068-62be-4980-9800-079aede03d4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637585.1_52067_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:17,881] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:17,884] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:17,885] [INFO] Target genome list was writen to GCF_900637585.1_52067_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:17,899] [INFO] Task started: fastANI
[2024-01-24 14:31:17,900] [INFO] Running command: fastANI --query /var/lib/cwl/stga45cf031-63dc-4cd6-bedc-5c9b1822d337/GCF_900637585.1_52067_F01_genomic.fna.gz --refList GCF_900637585.1_52067_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637585.1_52067_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:26,547] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,557] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:26,558] [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_900637585.1	s__Legionella pascullei	100.0	1151	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.92	99.72	1.00	0.99	8	conclusive
GCA_000586315.1	s__Legionella fraseri	93.8165	1014	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.50	96.27	0.94	0.87	43	-
GCF_000008485.1	s__Legionella pneumophila	91.3112	1018	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.85	95.56	0.93	0.84	789	-
GCF_000770585.1	s__Legionella norrlandica	80.3675	553	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423305.1	s__Legionella moravica	78.5788	232	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_011764505.1	s__Legionella sp011764505	78.3513	210	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468135.1	s__Legionella santicrucis	78.3492	210	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001467955.1	s__Legionella quateirensis	78.2257	260	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.97	99.97	0.99	0.99	3	-
GCF_900639985.1	s__Legionella rowbothamii	78.1506	139	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004283175.1	s__Legionella longbeachae	77.9395	164	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCF_000373765.1	s__Legionella shakespearei	77.9344	199	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,559] [INFO] GTDB search result was written to GCF_900637585.1_52067_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:26,560] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:26,563] [INFO] DFAST_QC result json was written to GCF_900637585.1_52067_F01_genomic.fna/dqc_result.json
[2024-01-24 14:31:26,564] [INFO] DFAST_QC completed!
[2024-01-24 14:31:26,564] [INFO] Total running time: 0h0m57s