[2024-01-25 19:04:20,457] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:20,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:20,458] [INFO] DQC Reference Directory: /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference
[2024-01-25 19:04:21,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:21,596] [INFO] Task started: Prodigal
[2024-01-25 19:04:21,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg85414b43-c628-4478-840b-21e348238a63/GCF_003989745.1_ASM398974v1_genomic.fna.gz | prodigal -d GCF_003989745.1_ASM398974v1_genomic.fna/cds.fna -a GCF_003989745.1_ASM398974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:27,308] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:27,308] [INFO] Task started: HMMsearch
[2024-01-25 19:04:27,308] [INFO] Running command: hmmsearch --tblout GCF_003989745.1_ASM398974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/reference_markers.hmm GCF_003989745.1_ASM398974v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:27,509] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:27,511] [INFO] Found 6/6 markers.
[2024-01-25 19:04:27,534] [INFO] Query marker FASTA was written to GCF_003989745.1_ASM398974v1_genomic.fna/markers.fasta
[2024-01-25 19:04:27,534] [INFO] Task started: Blastn
[2024-01-25 19:04:27,534] [INFO] Running command: blastn -query GCF_003989745.1_ASM398974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/reference_markers.fasta -out GCF_003989745.1_ASM398974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:28,132] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:28,135] [INFO] Selected 26 target genomes.
[2024-01-25 19:04:28,135] [INFO] Target genome list was writen to GCF_003989745.1_ASM398974v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:28,187] [INFO] Task started: fastANI
[2024-01-25 19:04:28,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg85414b43-c628-4478-840b-21e348238a63/GCF_003989745.1_ASM398974v1_genomic.fna.gz --refList GCF_003989745.1_ASM398974v1_genomic.fna/target_genomes.txt --output GCF_003989745.1_ASM398974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:40,392] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:40,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:40,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:40,406] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:40,406] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:40,406] [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 septentrionalis	strain=km711	GCA_003989745.1	2498109	2498109	type	True	100.0	836	842	95	conclusive
Legionella jordanis	strain=ATCC 33623	GCA_001648675.1	456	456	type	True	81.0879	80	842	95	below_threshold
Legionella jordanis	strain=BL-540	GCA_001467765.1	456	456	type	True	81.0236	83	842	95	below_threshold
Legionella jordanis	strain=NCTC11533	GCA_900637635.1	456	456	type	True	80.9626	84	842	95	below_threshold
Legionella gratiana	strain=NCTC12388	GCA_900452545.1	45066	45066	type	True	80.1665	64	842	95	below_threshold
Legionella gratiana	strain=Lyon 8420412	GCA_900639855.1	45066	45066	type	True	80.0971	65	842	95	below_threshold
Legionella gratiana	strain=Lyon 8420412	GCA_001467695.1	45066	45066	type	True	80.0162	64	842	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_900640205.1	455	455	type	True	78.0918	76	842	95	below_threshold
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	78.0497	80	842	95	below_threshold
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_001467745.1	455	455	type	True	77.9969	79	842	95	below_threshold
Legionella yabuuchiae	strain=OA1-2	GCA_900640115.1	376727	376727	type	True	77.7655	67	842	95	below_threshold
Legionella oakridgensis	strain=Oak Ridge-10	GCA_001467925.1	29423	29423	type	True	77.2606	112	842	95	below_threshold
Legionella oakridgensis	strain=ATCC 33761 = DSM 21215; OR-10	GCA_000512355.1	29423	29423	type	True	77.2529	113	842	95	below_threshold
Legionella oakridgensis	strain=ATCC 33761	GCA_001648605.1	29423	29423	type	True	77.2071	112	842	95	below_threshold
Legionella feeleii	strain=NCTC12022	GCA_900452475.1	453	453	type	True	77.1305	64	842	95	below_threshold
Legionella cherrii	strain=NCTC11976	GCA_900635815.1	28084	28084	type	True	77.0714	58	842	95	below_threshold
Legionella cherrii	strain=ORW	GCA_001467035.1	28084	28084	type	True	77.0489	64	842	95	below_threshold
Legionella lansingensis	strain=ATCC 49751	GCA_001467795.1	45067	45067	type	True	76.9945	54	842	95	below_threshold
Legionella cherrii	strain=ORW	GCA_900640085.1	28084	28084	type	True	76.8712	58	842	95	below_threshold
Legionella cherrii	strain=DSM 19213	GCA_000621385.1	28084	28084	type	True	76.865	56	842	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:40,407] [INFO] DFAST Taxonomy check result was written to GCF_003989745.1_ASM398974v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:40,408] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:40,408] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:40,408] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/checkm_data
[2024-01-25 19:04:40,409] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:40,437] [INFO] Task started: CheckM
[2024-01-25 19:04:40,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003989745.1_ASM398974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003989745.1_ASM398974v1_genomic.fna/checkm_input GCF_003989745.1_ASM398974v1_genomic.fna/checkm_result
[2024-01-25 19:05:02,233] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:02,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:02,257] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:02,258] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:02,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003989745.1_ASM398974v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:02,258] [INFO] Task started: Blastn
[2024-01-25 19:05:02,258] [INFO] Running command: blastn -query GCF_003989745.1_ASM398974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46d50da9-d628-4be2-8881-46caf7b4b4fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003989745.1_ASM398974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:03,317] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:03,320] [INFO] Selected 26 target genomes.
[2024-01-25 19:05:03,320] [INFO] Target genome list was writen to GCF_003989745.1_ASM398974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:03,347] [INFO] Task started: fastANI
[2024-01-25 19:05:03,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg85414b43-c628-4478-840b-21e348238a63/GCF_003989745.1_ASM398974v1_genomic.fna.gz --refList GCF_003989745.1_ASM398974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003989745.1_ASM398974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:17,284] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:17,295] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:17,295] [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_003989745.1	s__Legionella_A septentrionalis	100.0	836	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.39	99.22	0.94	0.93	4	conclusive
GCF_900637635.1	s__Tatlockia jordanis	80.9626	84	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.91	99.59	0.99	0.98	6	-
GCF_900639915.1	s__Legionella_A nagasakiensis	80.3133	111	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467695.1	s__Legionella gratiana	80.0162	64	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
GCA_002352055.1	s__Legionella sp002352055	78.8962	52	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452385.1	s__Tatlockia donaldsonii	78.205	67	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468035.1	s__Legionella tucsonensis	78.1216	58	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001467745.1	s__Tatlockia jamestowniensis	77.9969	79	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	-
GCF_900640115.1	s__Legionella_A yabuuchiae	77.7655	67	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900452865.1	s__Legionella_C taurinensis	77.5163	72	842	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_900167045.1	s__Tatlockia maceachernii	77.3218	73	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.96	0.99	0.99	4	-
GCF_000512355.1	s__Legionella_A oakridgensis	77.2529	113	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_A	95.0	99.85	99.51	0.97	0.90	5	-
GCF_900640175.1	s__Tatlockia sp900640175	77.182	65	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900639985.1	s__Legionella rowbothamii	77.1721	55	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187355.1	s__Tatlockia lansingensis	77.0934	54	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	-
GCF_900635815.1	s__Legionella cherrii	77.0714	58	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCF_000953135.1	s__Legionella fallonii	76.658	61	842	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:17,297] [INFO] GTDB search result was written to GCF_003989745.1_ASM398974v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:17,298] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:17,301] [INFO] DFAST_QC result json was written to GCF_003989745.1_ASM398974v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:17,302] [INFO] DFAST_QC completed!
[2024-01-25 19:05:17,302] [INFO] Total running time: 0h0m57s