[2023-03-17 00:45:49,107] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:49,108] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:49,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference
[2023-03-17 00:45:50,191] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:50,191] [INFO] Task started: Prodigal
[2023-03-17 00:45:50,191] [INFO] Running command: cat /var/lib/cwl/stgcfcc6360-0f25-4c99-a0f7-6fe8694cf5e1/OceanDNA-a3875.fa | prodigal -d OceanDNA-a3875/cds.fna -a OceanDNA-a3875/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:45:57,689] [INFO] Task succeeded: Prodigal
[2023-03-17 00:45:57,690] [INFO] Task started: HMMsearch
[2023-03-17 00:45:57,690] [INFO] Running command: hmmsearch --tblout OceanDNA-a3875/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/reference_markers.hmm OceanDNA-a3875/protein.faa > /dev/null
[2023-03-17 00:45:57,857] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:45:57,857] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcfcc6360-0f25-4c99-a0f7-6fe8694cf5e1/OceanDNA-a3875.fa]
[2023-03-17 00:45:57,867] [INFO] Query marker FASTA was written to OceanDNA-a3875/markers.fasta
[2023-03-17 00:45:57,868] [INFO] Task started: Blastn
[2023-03-17 00:45:57,868] [INFO] Running command: blastn -query OceanDNA-a3875/markers.fasta -db /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/reference_markers.fasta -out OceanDNA-a3875/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:45:58,287] [INFO] Task succeeded: Blastn
[2023-03-17 00:45:58,288] [INFO] Selected 4 target genomes.
[2023-03-17 00:45:58,288] [INFO] Target genome list was writen to OceanDNA-a3875/target_genomes.txt
[2023-03-17 00:45:58,296] [INFO] Task started: fastANI
[2023-03-17 00:45:58,296] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfcc6360-0f25-4c99-a0f7-6fe8694cf5e1/OceanDNA-a3875.fa --refList OceanDNA-a3875/target_genomes.txt --output OceanDNA-a3875/fastani_result.tsv --threads 1
[2023-03-17 00:45:59,599] [INFO] Task succeeded: fastANI
[2023-03-17 00:45:59,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:45:59,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:45:59,600] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:45:59,600] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:45:59,600] [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
--------------------------------------------------------------------------------
[2023-03-17 00:45:59,600] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3875/tc_result.tsv
[2023-03-17 00:45:59,600] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:45:59,600] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:45:59,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/checkm_data
[2023-03-17 00:45:59,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:45:59,736] [INFO] Task started: CheckM
[2023-03-17 00:45:59,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3875/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3875/checkm_input OceanDNA-a3875/checkm_result
[2023-03-17 00:46:25,017] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:25,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:25,019] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:25,019] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:25,019] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3875/markers.fasta)
[2023-03-17 00:46:25,019] [INFO] Task started: Blastn
[2023-03-17 00:46:25,019] [INFO] Running command: blastn -query OceanDNA-a3875/markers.fasta -db /var/lib/cwl/stg25668347-0994-4206-a899-fccd6afc0ae4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3875/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:26,165] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:26,166] [INFO] Selected 6 target genomes.
[2023-03-17 00:46:26,166] [INFO] Target genome list was writen to OceanDNA-a3875/target_genomes_gtdb.txt
[2023-03-17 00:46:26,359] [INFO] Task started: fastANI
[2023-03-17 00:46:26,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfcc6360-0f25-4c99-a0f7-6fe8694cf5e1/OceanDNA-a3875.fa --refList OceanDNA-a3875/target_genomes_gtdb.txt --output OceanDNA-a3875/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:28,173] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:28,178] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:46:28,178] [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_002497245.1	s__MGIIb-O2 sp002497245	99.8302	424	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	conclusive
GCA_902593945.1	s__MGIIb-O2 sp902593945	88.4005	334	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002504905.1	s__MGIIb-O2 sp002504905	83.6152	387	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	-
GCA_002498985.1	s__MGIIb-O2 sp002498985	82.8174	304	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.30	95.20	0.78	0.62	4	-
GCA_002495525.1	s__MGIIb-O2 sp002495525	82.701	357	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.21	96.68	0.79	0.75	3	-
GCA_002685315.1	s__MGIIb-O2 sp002685315	82.5193	239	462	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:28,178] [INFO] GTDB search result was written to OceanDNA-a3875/result_gtdb.tsv
[2023-03-17 00:46:28,178] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:28,179] [INFO] DFAST_QC result json was written to OceanDNA-a3875/dqc_result.json
[2023-03-17 00:46:28,179] [INFO] DFAST_QC completed!
[2023-03-17 00:46:28,179] [INFO] Total running time: 0h0m39s