[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,142] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,142] [INFO] DQC Reference Directory: /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference
[2024-01-25 17:34:09,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,030] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,030] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e72efb2-be3d-4f9f-940d-e7f57c153e02/GCF_001467545.1_ASM146754v1_genomic.fna.gz | prodigal -d GCF_001467545.1_ASM146754v1_genomic.fna/cds.fna -a GCF_001467545.1_ASM146754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:16,035] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:16,035] [INFO] Task started: HMMsearch
[2024-01-25 17:34:16,035] [INFO] Running command: hmmsearch --tblout GCF_001467545.1_ASM146754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/reference_markers.hmm GCF_001467545.1_ASM146754v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:16,270] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:16,271] [INFO] Found 6/6 markers.
[2024-01-25 17:34:16,301] [INFO] Query marker FASTA was written to GCF_001467545.1_ASM146754v1_genomic.fna/markers.fasta
[2024-01-25 17:34:16,301] [INFO] Task started: Blastn
[2024-01-25 17:34:16,301] [INFO] Running command: blastn -query GCF_001467545.1_ASM146754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/reference_markers.fasta -out GCF_001467545.1_ASM146754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:16,932] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:16,935] [INFO] Selected 9 target genomes.
[2024-01-25 17:34:16,935] [INFO] Target genome list was writen to GCF_001467545.1_ASM146754v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:16,960] [INFO] Task started: fastANI
[2024-01-25 17:34:16,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e72efb2-be3d-4f9f-940d-e7f57c153e02/GCF_001467545.1_ASM146754v1_genomic.fna.gz --refList GCF_001467545.1_ASM146754v1_genomic.fna/target_genomes.txt --output GCF_001467545.1_ASM146754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:25,540] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:25,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:25,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:25,547] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:25,547] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:25,547] [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 cincinnatiensis	strain=CDC#72-OH-14	GCA_001467545.1	28085	28085	type	True	100.0	1329	1329	95	conclusive
Legionella cincinnatiensis	strain=NCTC12438	GCA_900452415.1	28085	28085	type	True	99.9723	1327	1329	95	conclusive
Legionella santicrucis	strain=SC-63-C7	GCA_900639975.1	45074	45074	type	True	90.7918	1077	1329	95	below_threshold
Legionella santicrucis	strain=SC-63-C7	GCA_001468135.1	45074	45074	type	True	90.7366	1095	1329	95	below_threshold
Legionella sainthelensi	strain=Mt.St.Helens-4	GCA_001468105.1	28087	28087	type	True	88.1734	1070	1329	95	below_threshold
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	87.953	1039	1329	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:25,548] [INFO] DFAST Taxonomy check result was written to GCF_001467545.1_ASM146754v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:25,549] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:25,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:25,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/checkm_data
[2024-01-25 17:34:25,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:25,590] [INFO] Task started: CheckM
[2024-01-25 17:34:25,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001467545.1_ASM146754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001467545.1_ASM146754v1_genomic.fna/checkm_input GCF_001467545.1_ASM146754v1_genomic.fna/checkm_result
[2024-01-25 17:34:50,931] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:50,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:50,958] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:50,958] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:50,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001467545.1_ASM146754v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:50,959] [INFO] Task started: Blastn
[2024-01-25 17:34:50,959] [INFO] Running command: blastn -query GCF_001467545.1_ASM146754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea82f557-c59a-4032-9208-2198e0644917/dqc_reference/reference_markers_gtdb.fasta -out GCF_001467545.1_ASM146754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:51,955] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:51,958] [INFO] Selected 5 target genomes.
[2024-01-25 17:34:51,958] [INFO] Target genome list was writen to GCF_001467545.1_ASM146754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:51,962] [INFO] Task started: fastANI
[2024-01-25 17:34:51,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e72efb2-be3d-4f9f-940d-e7f57c153e02/GCF_001467545.1_ASM146754v1_genomic.fna.gz --refList GCF_001467545.1_ASM146754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001467545.1_ASM146754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:34:57,787] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:57,793] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:34:57,793] [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_900452415.1	s__Legionella cincinnatiensis	99.9723	1327	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_001468135.1	s__Legionella santicrucis	90.7823	1090	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.96	99.96	0.98	0.98	2	-
GCF_900637685.1	s__Legionella sainthelensi	88.1479	1074	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	97.79	95.71	0.95	0.89	8	-
GCA_004283175.1	s__Legionella longbeachae	87.9882	1012	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCF_001467695.1	s__Legionella gratiana	86.2337	981	1329	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:34:57,794] [INFO] GTDB search result was written to GCF_001467545.1_ASM146754v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:34:57,795] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:34:57,797] [INFO] DFAST_QC result json was written to GCF_001467545.1_ASM146754v1_genomic.fna/dqc_result.json
[2024-01-25 17:34:57,798] [INFO] DFAST_QC completed!
[2024-01-25 17:34:57,798] [INFO] Total running time: 0h0m51s