[2024-01-25 18:11:21,093] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:21,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:21,095] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference
[2024-01-25 18:11:22,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:22,223] [INFO] Task started: Prodigal
[2024-01-25 18:11:22,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg6729326c-8d6f-456b-9396-f6c49da6b3fb/GCF_001468125.1_ASM146812v1_genomic.fna.gz | prodigal -d GCF_001468125.1_ASM146812v1_genomic.fna/cds.fna -a GCF_001468125.1_ASM146812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:29,507] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:29,507] [INFO] Task started: HMMsearch
[2024-01-25 18:11:29,507] [INFO] Running command: hmmsearch --tblout GCF_001468125.1_ASM146812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/reference_markers.hmm GCF_001468125.1_ASM146812v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:29,730] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:29,731] [INFO] Found 6/6 markers.
[2024-01-25 18:11:29,757] [INFO] Query marker FASTA was written to GCF_001468125.1_ASM146812v1_genomic.fna/markers.fasta
[2024-01-25 18:11:29,757] [INFO] Task started: Blastn
[2024-01-25 18:11:29,757] [INFO] Running command: blastn -query GCF_001468125.1_ASM146812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/reference_markers.fasta -out GCF_001468125.1_ASM146812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:30,417] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:30,420] [INFO] Selected 6 target genomes.
[2024-01-25 18:11:30,420] [INFO] Target genome list was writen to GCF_001468125.1_ASM146812v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:30,425] [INFO] Task started: fastANI
[2024-01-25 18:11:30,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg6729326c-8d6f-456b-9396-f6c49da6b3fb/GCF_001468125.1_ASM146812v1_genomic.fna.gz --refList GCF_001468125.1_ASM146812v1_genomic.fna/target_genomes.txt --output GCF_001468125.1_ASM146812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:34,675] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:34,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:34,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:34,681] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:11:34,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:34,681] [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 rubrilucens	strain=WA-270A-C2	GCA_001468125.1	458	458	type	True	100.0	1034	1034	95	conclusive
Legionella rubrilucens	strain=WA-270A-C2	GCA_900640015.1	458	458	type	True	99.99	1026	1034	95	conclusive
Legionella taurinensis	strain=NCTC13314	GCA_900452865.1	70611	70611	type	True	92.0677	924	1034	95	below_threshold
Legionella erythra	strain=SE-32A-C8	GCA_900639845.1	448	448	type	True	84.1265	819	1034	95	below_threshold
Legionella erythra	strain=SE-32A-C8	GCA_001467615.1	448	448	type	True	84.1162	832	1034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:34,683] [INFO] DFAST Taxonomy check result was written to GCF_001468125.1_ASM146812v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:34,684] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:34,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:34,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/checkm_data
[2024-01-25 18:11:34,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:34,718] [INFO] Task started: CheckM
[2024-01-25 18:11:34,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001468125.1_ASM146812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001468125.1_ASM146812v1_genomic.fna/checkm_input GCF_001468125.1_ASM146812v1_genomic.fna/checkm_result
[2024-01-25 18:12:00,613] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:00,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:00,631] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:00,632] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:00,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001468125.1_ASM146812v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:00,632] [INFO] Task started: Blastn
[2024-01-25 18:12:00,632] [INFO] Running command: blastn -query GCF_001468125.1_ASM146812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5910415-0259-452f-b259-69d66bb102b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001468125.1_ASM146812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:01,786] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:01,788] [INFO] Selected 10 target genomes.
[2024-01-25 18:12:01,788] [INFO] Target genome list was writen to GCF_001468125.1_ASM146812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:01,810] [INFO] Task started: fastANI
[2024-01-25 18:12:01,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg6729326c-8d6f-456b-9396-f6c49da6b3fb/GCF_001468125.1_ASM146812v1_genomic.fna.gz --refList GCF_001468125.1_ASM146812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001468125.1_ASM146812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:08,580] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:08,586] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:08,586] [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_001468125.1	s__Legionella_C rubrilucens	100.0	1034	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_900452865.1	s__Legionella_C taurinensis	92.0926	922	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.63	99.52	0.96	0.95	16	-
GCF_016864235.1	s__Legionella_C sp016864235	90.9979	943	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467615.1	s__Legionella_C erythra	84.1227	831	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.95	99.95	0.98	0.98	2	-
GCF_000621525.1	s__Tatlockia fairfieldensis	82.2997	105	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900637635.1	s__Tatlockia jordanis	80.403	99	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_900452385.1	s__Tatlockia donaldsonii	78.0014	88	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900461555.1	s__Legionella_C quinlivanii	77.5204	94	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.97	99.95	0.99	0.98	4	-
GCF_000373765.1	s__Legionella shakespearei	77.1025	71	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:08,587] [INFO] GTDB search result was written to GCF_001468125.1_ASM146812v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:08,588] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:08,590] [INFO] DFAST_QC result json was written to GCF_001468125.1_ASM146812v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:08,590] [INFO] DFAST_QC completed!
[2024-01-25 18:12:08,590] [INFO] Total running time: 0h0m47s