[2024-01-24 10:57:39,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:39,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:39,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference
[2024-01-24 10:57:40,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,383] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg35770012-8b3e-4076-9963-9bf613dad121/GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna.gz | prodigal -d GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/cds.fna -a GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:48,279] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:48,279] [INFO] Task started: HMMsearch
[2024-01-24 10:57:48,280] [INFO] Running command: hmmsearch --tblout GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/reference_markers.hmm GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:48,547] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:48,549] [INFO] Found 6/6 markers.
[2024-01-24 10:57:48,583] [INFO] Query marker FASTA was written to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/markers.fasta
[2024-01-24 10:57:48,583] [INFO] Task started: Blastn
[2024-01-24 10:57:48,583] [INFO] Running command: blastn -query GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/reference_markers.fasta -out GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:49,264] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:49,267] [INFO] Selected 9 target genomes.
[2024-01-24 10:57:49,268] [INFO] Target genome list was writen to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:49,273] [INFO] Task started: fastANI
[2024-01-24 10:57:49,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg35770012-8b3e-4076-9963-9bf613dad121/GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna.gz --refList GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/target_genomes.txt --output GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:57,667] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:57,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:57,669] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:57,680] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 10:57:57,680] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:57,680] [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 sainthelensi	strain=MSH-4	GCA_900640185.1	28087	28087	type	True	100.0	1335	1337	95	conclusive
Legionella sainthelensi	strain=ATCC 35248	GCA_000621685.1	28087	28087	type	True	99.9963	1331	1337	95	conclusive
Legionella sainthelensi	strain=NCTC11988	GCA_900637685.1	28087	28087	type	True	99.9886	1336	1337	95	conclusive
Legionella sainthelensi	strain=Mt.St.Helens-4	GCA_001468105.1	28087	28087	type	True	99.9848	1334	1337	95	conclusive
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	88.8261	1097	1337	95	below_threshold
Legionella santicrucis	strain=SC-63-C7	GCA_001468135.1	45074	45074	type	True	88.3321	1083	1337	95	below_threshold
Legionella cincinnatiensis	strain=NCTC12438	GCA_900452415.1	28085	28085	type	True	88.087	1083	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:57,682] [INFO] DFAST Taxonomy check result was written to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:57,683] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:57,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:57,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/checkm_data
[2024-01-24 10:57:57,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:57,725] [INFO] Task started: CheckM
[2024-01-24 10:57:57,725] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/checkm_input GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/checkm_result
[2024-01-24 10:58:27,569] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:27,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:27,588] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:27,588] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:27,589] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:27,589] [INFO] Task started: Blastn
[2024-01-24 10:58:27,590] [INFO] Running command: blastn -query GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926138e6-73f0-4fd7-88a0-91c6940bde73/dqc_reference/reference_markers_gtdb.fasta -out GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:28,605] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:28,609] [INFO] Selected 5 target genomes.
[2024-01-24 10:58:28,610] [INFO] Target genome list was writen to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:28,615] [INFO] Task started: fastANI
[2024-01-24 10:58:28,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg35770012-8b3e-4076-9963-9bf613dad121/GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna.gz --refList GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:34,324] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:34,334] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:34,335] [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_900637685.1	s__Legionella sainthelensi	99.9886	1336	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	conclusive
GCA_004283175.1	s__Legionella longbeachae	88.8255	1085	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCF_001468135.1	s__Legionella santicrucis	88.3451	1082	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_900452415.1	s__Legionella cincinnatiensis	88.0849	1083	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001467695.1	s__Legionella gratiana	84.3189	926	1337	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:34,337] [INFO] GTDB search result was written to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:34,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:34,340] [INFO] DFAST_QC result json was written to GCF_900640185.1_Leg_sainthelensi_MSH-4.v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:34,340] [INFO] DFAST_QC completed!
[2024-01-24 10:58:34,341] [INFO] Total running time: 0h0m55s