[2024-01-24 14:56:23,780] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,782] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference
[2024-01-24 14:56:26,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,561] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,562] [INFO] Running command: gunzip -c /var/lib/cwl/stg2829304e-4823-4dc9-8804-eb2f0cadbb36/GCF_001468065.1_ASM146806v1_genomic.fna.gz | prodigal -d GCF_001468065.1_ASM146806v1_genomic.fna/cds.fna -a GCF_001468065.1_ASM146806v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:35,351] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:35,352] [INFO] Task started: HMMsearch
[2024-01-24 14:56:35,352] [INFO] Running command: hmmsearch --tblout GCF_001468065.1_ASM146806v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/reference_markers.hmm GCF_001468065.1_ASM146806v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:35,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:35,742] [INFO] Found 6/6 markers.
[2024-01-24 14:56:35,783] [INFO] Query marker FASTA was written to GCF_001468065.1_ASM146806v1_genomic.fna/markers.fasta
[2024-01-24 14:56:35,783] [INFO] Task started: Blastn
[2024-01-24 14:56:35,784] [INFO] Running command: blastn -query GCF_001468065.1_ASM146806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/reference_markers.fasta -out GCF_001468065.1_ASM146806v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:37,009] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:37,012] [INFO] Selected 9 target genomes.
[2024-01-24 14:56:37,012] [INFO] Target genome list was writen to GCF_001468065.1_ASM146806v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:37,516] [INFO] Task started: fastANI
[2024-01-24 14:56:37,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg2829304e-4823-4dc9-8804-eb2f0cadbb36/GCF_001468065.1_ASM146806v1_genomic.fna.gz --refList GCF_001468065.1_ASM146806v1_genomic.fna/target_genomes.txt --output GCF_001468065.1_ASM146806v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:46,287] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:46,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:46,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:46,300] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:46,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:46,301] [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 steigerwaltii	strain=SC-18-C9	GCA_001468065.1	460	460	type	True	100.0	1295	1295	95	conclusive
Legionella steigerwaltii	strain=NCTC11991	GCA_900452835.1	460	460	type	True	99.9908	1291	1295	95	conclusive
Legionella steigerwaltii	strain=SC-18-C9	GCA_900640025.1	460	460	type	True	99.9826	1283	1295	95	conclusive
Legionella cherrii	strain=ORW	GCA_001467035.1	28084	28084	type	True	85.7365	1010	1295	95	below_threshold
Legionella cherrii	strain=ORW	GCA_900640085.1	28084	28084	type	True	85.5856	992	1295	95	below_threshold
Legionella steelei	strain=IMVS3376	GCA_001468005.1	947033	947033	type	True	85.2282	1010	1295	95	below_threshold
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	82.5863	871	1295	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	77.9831	268	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:46,308] [INFO] DFAST Taxonomy check result was written to GCF_001468065.1_ASM146806v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:46,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:46,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:46,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/checkm_data
[2024-01-24 14:56:46,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:46,353] [INFO] Task started: CheckM
[2024-01-24 14:56:46,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001468065.1_ASM146806v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001468065.1_ASM146806v1_genomic.fna/checkm_input GCF_001468065.1_ASM146806v1_genomic.fna/checkm_result
[2024-01-24 14:57:18,854] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:18,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:18,878] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:18,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:18,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001468065.1_ASM146806v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:18,879] [INFO] Task started: Blastn
[2024-01-24 14:57:18,880] [INFO] Running command: blastn -query GCF_001468065.1_ASM146806v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde55ccf1-923b-4f10-9825-643a701307b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001468065.1_ASM146806v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:19,927] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:19,935] [INFO] Selected 10 target genomes.
[2024-01-24 14:57:19,935] [INFO] Target genome list was writen to GCF_001468065.1_ASM146806v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:19,942] [INFO] Task started: fastANI
[2024-01-24 14:57:19,942] [INFO] Running command: fastANI --query /var/lib/cwl/stg2829304e-4823-4dc9-8804-eb2f0cadbb36/GCF_001468065.1_ASM146806v1_genomic.fna.gz --refList GCF_001468065.1_ASM146806v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001468065.1_ASM146806v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:29,520] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:29,535] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:29,535] [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_001468065.1	s__Legionella steigerwaltii	100.0	1295	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCF_900635815.1	s__Legionella cherrii	85.5904	996	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_001468005.1	s__Legionella steelei	85.2282	1010	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_001467525.1	s__Legionella anisa	82.5827	872	1295	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	82.4677	827	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_900156395.1	s__Legionella gormanii	82.3063	765	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.78	98.94	0.98	0.92	6	-
GCF_001468035.1	s__Legionella tucsonensis	82.1531	767	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014109805.1	s__Legionella sp014109805	81.9006	831	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003184185.1	s__Legionella qingyii	81.8114	780	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.76	0.97	0.97	3	-
GCF_000236165.1	s__Legionella dumoffii	81.7679	771	1295	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.81	99.55	0.97	0.94	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:29,537] [INFO] GTDB search result was written to GCF_001468065.1_ASM146806v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:29,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:29,541] [INFO] DFAST_QC result json was written to GCF_001468065.1_ASM146806v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:29,541] [INFO] DFAST_QC completed!
[2024-01-24 14:57:29,541] [INFO] Total running time: 0h1m6s