[2023-03-19 04:29:37,740] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:29:37,740] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:29:37,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference
[2023-03-19 04:29:38,862] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:29:38,863] [INFO] Task started: Prodigal
[2023-03-19 04:29:38,864] [INFO] Running command: cat /var/lib/cwl/stg7e54a7fd-4a45-414f-94a1-924b94439f1e/OceanDNA-b35953.fa | prodigal -d OceanDNA-b35953/cds.fna -a OceanDNA-b35953/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:29:49,418] [INFO] Task succeeded: Prodigal
[2023-03-19 04:29:49,418] [INFO] Task started: HMMsearch
[2023-03-19 04:29:49,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b35953/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/reference_markers.hmm OceanDNA-b35953/protein.faa > /dev/null
[2023-03-19 04:29:49,601] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:29:49,602] [INFO] Found 6/6 markers.
[2023-03-19 04:29:49,616] [INFO] Query marker FASTA was written to OceanDNA-b35953/markers.fasta
[2023-03-19 04:29:49,616] [INFO] Task started: Blastn
[2023-03-19 04:29:49,616] [INFO] Running command: blastn -query OceanDNA-b35953/markers.fasta -db /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/reference_markers.fasta -out OceanDNA-b35953/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:29:50,199] [INFO] Task succeeded: Blastn
[2023-03-19 04:29:50,200] [INFO] Selected 32 target genomes.
[2023-03-19 04:29:50,200] [INFO] Target genome list was writen to OceanDNA-b35953/target_genomes.txt
[2023-03-19 04:29:50,219] [INFO] Task started: fastANI
[2023-03-19 04:29:50,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e54a7fd-4a45-414f-94a1-924b94439f1e/OceanDNA-b35953.fa --refList OceanDNA-b35953/target_genomes.txt --output OceanDNA-b35953/fastani_result.tsv --threads 1
[2023-03-19 04:30:04,592] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:04,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:30:04,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:30:04,597] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:30:04,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:30:04,597] [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 nautarum	strain=1224	GCA_900639935.1	45070	45070	type	True	77.2903	52	650	95	below_threshold
Legionella nautarum	strain=ATCC 49506	GCA_001467895.1	45070	45070	type	True	77.2333	52	650	95	below_threshold
Legionella busanensis	strain=NCTC13316	GCA_900461525.1	190655	190655	type	True	76.5427	59	650	95	below_threshold
Legionella gresilensis	strain=Greoux 11D13	GCA_900639865.1	91823	91823	type	True	76.1921	51	650	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:30:04,597] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35953/tc_result.tsv
[2023-03-19 04:30:04,597] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:30:04,597] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:30:04,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/checkm_data
[2023-03-19 04:30:04,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:30:04,601] [INFO] Task started: CheckM
[2023-03-19 04:30:04,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35953/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35953/checkm_input OceanDNA-b35953/checkm_result
[2023-03-19 04:30:35,030] [INFO] Task succeeded: CheckM
[2023-03-19 04:30:35,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:30:35,032] [INFO] ===== Completeness check finished =====
[2023-03-19 04:30:35,032] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:30:35,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35953/markers.fasta)
[2023-03-19 04:30:35,033] [INFO] Task started: Blastn
[2023-03-19 04:30:35,033] [INFO] Running command: blastn -query OceanDNA-b35953/markers.fasta -db /var/lib/cwl/stg0bd32ea5-0e09-4db6-a76a-7b17f0cb5179/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35953/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:30:35,914] [INFO] Task succeeded: Blastn
[2023-03-19 04:30:35,915] [INFO] Selected 28 target genomes.
[2023-03-19 04:30:35,916] [INFO] Target genome list was writen to OceanDNA-b35953/target_genomes_gtdb.txt
[2023-03-19 04:30:35,939] [INFO] Task started: fastANI
[2023-03-19 04:30:35,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e54a7fd-4a45-414f-94a1-924b94439f1e/OceanDNA-b35953.fa --refList OceanDNA-b35953/target_genomes_gtdb.txt --output OceanDNA-b35953/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:30:49,541] [INFO] Task succeeded: fastANI
[2023-03-19 04:30:49,545] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:30:49,545] [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
GCA_002863045.1	s__GCA-2863045 sp002863045	98.4544	537	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__GCA-2863045	95.0	98.31	98.18	0.88	0.83	7	conclusive
GCF_001467895.1	s__Tatlockia nautarum	77.2896	51	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Tatlockia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900461525.1	s__Legionella_C busanensis	76.5804	58	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900639865.1	s__Legionella_C gresilensis	76.1921	51	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:30:49,545] [INFO] GTDB search result was written to OceanDNA-b35953/result_gtdb.tsv
[2023-03-19 04:30:49,545] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:30:49,546] [INFO] DFAST_QC result json was written to OceanDNA-b35953/dqc_result.json
[2023-03-19 04:30:49,546] [INFO] DFAST_QC completed!
[2023-03-19 04:30:49,546] [INFO] Total running time: 0h1m12s