[2023-03-18 07:29:30,336] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,336] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg7a845867-32ef-4d12-aef3-73bb2063b37e/OceanDNA-a2998.fa | prodigal -d OceanDNA-a2998/cds.fna -a OceanDNA-a2998/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:42,245] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:42,245] [INFO] Task started: HMMsearch
[2023-03-18 07:29:42,245] [INFO] Running command: hmmsearch --tblout OceanDNA-a2998/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/reference_markers.hmm OceanDNA-a2998/protein.faa > /dev/null
[2023-03-18 07:29:42,415] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:42,416] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7a845867-32ef-4d12-aef3-73bb2063b37e/OceanDNA-a2998.fa]
[2023-03-18 07:29:42,427] [INFO] Query marker FASTA was written to OceanDNA-a2998/markers.fasta
[2023-03-18 07:29:42,428] [INFO] Task started: Blastn
[2023-03-18 07:29:42,428] [INFO] Running command: blastn -query OceanDNA-a2998/markers.fasta -db /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/reference_markers.fasta -out OceanDNA-a2998/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:42,857] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:42,857] [INFO] Selected 5 target genomes.
[2023-03-18 07:29:42,858] [INFO] Target genome list was writen to OceanDNA-a2998/target_genomes.txt
[2023-03-18 07:29:42,861] [INFO] Task started: fastANI
[2023-03-18 07:29:42,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a845867-32ef-4d12-aef3-73bb2063b37e/OceanDNA-a2998.fa --refList OceanDNA-a2998/target_genomes.txt --output OceanDNA-a2998/fastani_result.tsv --threads 1
[2023-03-18 07:29:46,384] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:46,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:46,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:46,385] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:46,385] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:46,385] [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
--------------------------------------------------------------------------------
[2023-03-18 07:29:46,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2998/tc_result.tsv
[2023-03-18 07:29:46,385] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:46,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:46,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/checkm_data
[2023-03-18 07:29:46,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:46,392] [INFO] Task started: CheckM
[2023-03-18 07:29:46,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2998/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2998/checkm_input OceanDNA-a2998/checkm_result
[2023-03-18 07:30:17,574] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:17,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:17,577] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:17,577] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:17,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2998/markers.fasta)
[2023-03-18 07:30:17,577] [INFO] Task started: Blastn
[2023-03-18 07:30:17,577] [INFO] Running command: blastn -query OceanDNA-a2998/markers.fasta -db /var/lib/cwl/stgb2bf29c8-4299-4946-9e59-89050506d891/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2998/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:18,015] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:18,016] [INFO] Selected 8 target genomes.
[2023-03-18 07:30:18,016] [INFO] Target genome list was writen to OceanDNA-a2998/target_genomes_gtdb.txt
[2023-03-18 07:30:18,148] [INFO] Task started: fastANI
[2023-03-18 07:30:18,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a845867-32ef-4d12-aef3-73bb2063b37e/OceanDNA-a2998.fa --refList OceanDNA-a2998/target_genomes_gtdb.txt --output OceanDNA-a2998/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:20,960] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:20,965] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:30:20,965] [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_016778305.1	s__Poseidonia sp016778305	98.8703	506	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.89	99.85	0.97	0.96	5	conclusive
GCA_003602485.1	s__Poseidonia sp003602485	84.0748	413	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002494645.1	s__Poseidonia sp002494645	81.5538	406	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.84	99.84	0.96	0.96	2	-
GCA_902625885.1	s__Poseidonia sp902625885	77.2001	78	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728035.1	s__Poseidonia sp002728035	77.167	117	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.50	96.50	0.78	0.78	2	-
GCA_002497765.1	s__Poseidonia sp002497765	77.1413	107	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.70	99.65	0.88	0.86	3	-
GCA_002689105.1	s__Poseidonia sp002689105	77.0176	101	531	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:20,966] [INFO] GTDB search result was written to OceanDNA-a2998/result_gtdb.tsv
[2023-03-18 07:30:20,966] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:20,966] [INFO] DFAST_QC result json was written to OceanDNA-a2998/dqc_result.json
[2023-03-18 07:30:20,967] [INFO] DFAST_QC completed!
[2023-03-18 07:30:20,967] [INFO] Total running time: 0h0m51s