[2024-01-24 11:44:23,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference
[2024-01-24 11:44:26,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,342] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg41bc837a-9fc8-425c-a154-39e4c508737c/GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna.gz | prodigal -d GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/cds.fna -a GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:33,751] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:33,752] [INFO] Task started: HMMsearch
[2024-01-24 11:44:33,752] [INFO] Running command: hmmsearch --tblout GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/reference_markers.hmm GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,048] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,079] [INFO] Query marker FASTA was written to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,080] [INFO] Task started: Blastn
[2024-01-24 11:44:34,080] [INFO] Running command: blastn -query GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/reference_markers.fasta -out GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:34,740] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:34,743] [INFO] Selected 10 target genomes.
[2024-01-24 11:44:34,744] [INFO] Target genome list was writen to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:34,785] [INFO] Task started: fastANI
[2024-01-24 11:44:34,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bc837a-9fc8-425c-a154-39e4c508737c/GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna.gz --refList GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/target_genomes.txt --output GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:41,604] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:41,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:41,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:41,619] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:44:41,619] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:41,619] [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 jamestowniensis	strain=JA-26-G1-E2	GCA_900640205.1	455	455	type	True	100.0	1122	1124	95	conclusive
Legionella jamestowniensis	strain=DSM 19215	GCA_900114725.1	455	455	type	True	99.9938	1122	1124	95	conclusive
Legionella jamestowniensis	strain=JA-26-G1-E2	GCA_001467745.1	455	455	type	True	99.9819	1095	1124	95	conclusive
Legionella clemsonensis	strain=CDC-D5610	GCA_002240035.1	1867846	1867846	type	True	83.1031	774	1124	95	below_threshold
Legionella hackeliae	strain=ATCC35250	GCA_000953655.1	449	449	type	True	79.6264	483	1124	95	below_threshold
Legionella brunensis	strain=ATCC 43878	GCA_001467025.1	29422	29422	type	True	79.5765	345	1124	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	77.8838	99	1124	95	below_threshold
Legionella gresilensis	strain=Greoux 11D13	GCA_900639865.1	91823	91823	type	True	76.8971	102	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:41,621] [INFO] DFAST Taxonomy check result was written to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:41,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:41,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:41,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/checkm_data
[2024-01-24 11:44:41,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:41,659] [INFO] Task started: CheckM
[2024-01-24 11:44:41,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/checkm_input GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/checkm_result
[2024-01-24 11:45:09,404] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:09,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:09,428] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:09,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:09,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:09,430] [INFO] Task started: Blastn
[2024-01-24 11:45:09,430] [INFO] Running command: blastn -query GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2429beea-62a0-42c2-8a89-a28b3a478396/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:10,430] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:10,436] [INFO] Selected 11 target genomes.
[2024-01-24 11:45:10,437] [INFO] Target genome list was writen to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:10,474] [INFO] Task started: fastANI
[2024-01-24 11:45:10,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg41bc837a-9fc8-425c-a154-39e4c508737c/GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna.gz --refList GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:17,115] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:17,127] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:17,128] [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_001467745.1	s__Tatlockia jamestowniensis	99.9819	1095	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.71	99.16	0.98	0.95	4	conclusive
GCF_002240035.1	s__Tatlockia clemsonensis	83.092	775	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953655.1	s__Tatlockia hackeliae	79.637	482	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.95	99.91	0.98	0.96	3	-
GCF_001467025.1	s__Tatlockia brunensis	79.5908	344	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900187355.1	s__Tatlockia lansingensis	77.7528	202	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.99	99.98	1.00	1.00	4	-
GCF_900452385.1	s__Tatlockia donaldsonii	77.7013	157	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467625.1	s__Tatlockia feeleii	77.5449	160	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.52	98.18	0.97	0.92	5	-
GCF_001468035.1	s__Legionella tucsonensis	77.2709	97	1124	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,129] [INFO] GTDB search result was written to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:17,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:17,132] [INFO] DFAST_QC result json was written to GCF_900640205.1_Leg_jamestowniensis_JA-26-G1-E2.v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:17,133] [INFO] DFAST_QC completed!
[2024-01-24 11:45:17,133] [INFO] Total running time: 0h0m53s