[2023-03-15 07:29:11,758] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:29:11,758] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:29:11,758] [INFO] DQC Reference Directory: /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference
[2023-03-15 07:29:13,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:29:13,587] [INFO] Task started: Prodigal
[2023-03-15 07:29:13,588] [INFO] Running command: cat /var/lib/cwl/stgdc9bbe47-03e2-46d7-bf4d-9f2a7f38e8be/OceanDNA-b37669.fa | prodigal -d OceanDNA-b37669/cds.fna -a OceanDNA-b37669/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:29:26,346] [INFO] Task succeeded: Prodigal
[2023-03-15 07:29:26,346] [INFO] Task started: HMMsearch
[2023-03-15 07:29:26,346] [INFO] Running command: hmmsearch --tblout OceanDNA-b37669/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/reference_markers.hmm OceanDNA-b37669/protein.faa > /dev/null
[2023-03-15 07:29:26,542] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:29:26,543] [INFO] Found 6/6 markers.
[2023-03-15 07:29:26,559] [INFO] Query marker FASTA was written to OceanDNA-b37669/markers.fasta
[2023-03-15 07:29:26,559] [INFO] Task started: Blastn
[2023-03-15 07:29:26,559] [INFO] Running command: blastn -query OceanDNA-b37669/markers.fasta -db /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/reference_markers.fasta -out OceanDNA-b37669/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:29:27,187] [INFO] Task succeeded: Blastn
[2023-03-15 07:29:27,188] [INFO] Selected 28 target genomes.
[2023-03-15 07:29:27,188] [INFO] Target genome list was writen to OceanDNA-b37669/target_genomes.txt
[2023-03-15 07:29:27,207] [INFO] Task started: fastANI
[2023-03-15 07:29:27,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9bbe47-03e2-46d7-bf4d-9f2a7f38e8be/OceanDNA-b37669.fa --refList OceanDNA-b37669/target_genomes.txt --output OceanDNA-b37669/fastani_result.tsv --threads 1
[2023-03-15 07:29:44,340] [INFO] Task succeeded: fastANI
[2023-03-15 07:29:44,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:29:44,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:29:44,345] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:29:44,345] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:29:44,345] [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
Aequoribacter fuscus	strain=IMCC3088	GCA_009910365.1	2518989	2518989	type	True	80.9263	86	710	95	below_threshold
Aequoribacter fuscus	strain=IMCC3088	GCA_000204315.2	2518989	2518989	type	True	80.1616	81	710	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:29:44,345] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37669/tc_result.tsv
[2023-03-15 07:29:44,345] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:29:44,345] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:29:44,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/checkm_data
[2023-03-15 07:29:44,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:29:44,350] [INFO] Task started: CheckM
[2023-03-15 07:29:44,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37669/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37669/checkm_input OceanDNA-b37669/checkm_result
[2023-03-15 07:30:20,230] [INFO] Task succeeded: CheckM
[2023-03-15 07:30:20,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:30:20,232] [INFO] ===== Completeness check finished =====
[2023-03-15 07:30:20,233] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:30:20,233] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37669/markers.fasta)
[2023-03-15 07:30:20,234] [INFO] Task started: Blastn
[2023-03-15 07:30:20,234] [INFO] Running command: blastn -query OceanDNA-b37669/markers.fasta -db /var/lib/cwl/stg984b7b3d-e388-4320-af0a-fd218312c896/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37669/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:30:21,235] [INFO] Task succeeded: Blastn
[2023-03-15 07:30:21,236] [INFO] Selected 28 target genomes.
[2023-03-15 07:30:21,236] [INFO] Target genome list was writen to OceanDNA-b37669/target_genomes_gtdb.txt
[2023-03-15 07:30:21,251] [INFO] Task started: fastANI
[2023-03-15 07:30:21,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc9bbe47-03e2-46d7-bf4d-9f2a7f38e8be/OceanDNA-b37669.fa --refList OceanDNA-b37669/target_genomes_gtdb.txt --output OceanDNA-b37669/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:30:35,197] [INFO] Task succeeded: fastANI
[2023-03-15 07:30:35,199] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:30:35,199] [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_003520285.1	s__Aequoribacter sp003520285	97.168	372	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Aequoribacter	95.0	97.57	97.32	0.79	0.72	5	conclusive
GCF_009910365.1	s__Aequoribacter fuscus	80.9263	86	710	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Aequoribacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-15 07:30:35,200] [INFO] GTDB search result was written to OceanDNA-b37669/result_gtdb.tsv
[2023-03-15 07:30:35,200] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:30:35,200] [INFO] DFAST_QC result json was written to OceanDNA-b37669/dqc_result.json
[2023-03-15 07:30:35,200] [INFO] DFAST_QC completed!
[2023-03-15 07:30:35,200] [INFO] Total running time: 0h1m23s