[2023-03-16 01:12:29,305] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:12:29,315] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:12:29,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference
[2023-03-16 01:12:30,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:12:30,461] [INFO] Task started: Prodigal
[2023-03-16 01:12:30,462] [INFO] Running command: cat /var/lib/cwl/stgde7d3950-930a-4a1d-92e7-ffe4e5fea850/OceanDNA-a1938.fa | prodigal -d OceanDNA-a1938/cds.fna -a OceanDNA-a1938/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:12:38,577] [INFO] Task succeeded: Prodigal
[2023-03-16 01:12:38,577] [INFO] Task started: HMMsearch
[2023-03-16 01:12:38,577] [INFO] Running command: hmmsearch --tblout OceanDNA-a1938/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/reference_markers.hmm OceanDNA-a1938/protein.faa > /dev/null
[2023-03-16 01:12:38,755] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:12:38,756] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgde7d3950-930a-4a1d-92e7-ffe4e5fea850/OceanDNA-a1938.fa]
[2023-03-16 01:12:38,815] [INFO] Query marker FASTA was written to OceanDNA-a1938/markers.fasta
[2023-03-16 01:12:38,816] [INFO] Task started: Blastn
[2023-03-16 01:12:38,816] [INFO] Running command: blastn -query OceanDNA-a1938/markers.fasta -db /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/reference_markers.fasta -out OceanDNA-a1938/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:12:39,262] [INFO] Task succeeded: Blastn
[2023-03-16 01:12:39,283] [INFO] Selected 5 target genomes.
[2023-03-16 01:12:39,284] [INFO] Target genome list was writen to OceanDNA-a1938/target_genomes.txt
[2023-03-16 01:12:39,312] [INFO] Task started: fastANI
[2023-03-16 01:12:39,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7d3950-930a-4a1d-92e7-ffe4e5fea850/OceanDNA-a1938.fa --refList OceanDNA-a1938/target_genomes.txt --output OceanDNA-a1938/fastani_result.tsv --threads 1
[2023-03-16 01:12:40,700] [INFO] Task succeeded: fastANI
[2023-03-16 01:12:40,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:12:40,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:12:40,700] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:12:40,700] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:12:40,701] [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
--------------------------------------------------------------------------------
[2023-03-16 01:12:40,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1938/tc_result.tsv
[2023-03-16 01:12:40,730] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:12:40,730] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:12:40,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/checkm_data
[2023-03-16 01:12:40,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:12:40,738] [INFO] Task started: CheckM
[2023-03-16 01:12:40,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1938/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1938/checkm_input OceanDNA-a1938/checkm_result
[2023-03-16 01:13:06,706] [INFO] Task succeeded: CheckM
[2023-03-16 01:13:06,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.63%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:13:06,748] [INFO] ===== Completeness check finished =====
[2023-03-16 01:13:06,748] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:13:06,748] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1938/markers.fasta)
[2023-03-16 01:13:06,749] [INFO] Task started: Blastn
[2023-03-16 01:13:06,749] [INFO] Running command: blastn -query OceanDNA-a1938/markers.fasta -db /var/lib/cwl/stg4e03d6ed-88cb-4ad4-ab54-131ff63112d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1938/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:13:07,157] [INFO] Task succeeded: Blastn
[2023-03-16 01:13:07,158] [INFO] Selected 10 target genomes.
[2023-03-16 01:13:07,158] [INFO] Target genome list was writen to OceanDNA-a1938/target_genomes_gtdb.txt
[2023-03-16 01:13:07,265] [INFO] Task started: fastANI
[2023-03-16 01:13:07,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgde7d3950-930a-4a1d-92e7-ffe4e5fea850/OceanDNA-a1938.fa --refList OceanDNA-a1938/target_genomes_gtdb.txt --output OceanDNA-a1938/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:13:10,323] [INFO] Task succeeded: fastANI
[2023-03-16 01:13:10,327] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:13:10,327] [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_003602415.1	s__MGIIa-K1 sp003602415	77.0595	118	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	76.9271	95	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710205.1	s__MGIIa-K1 sp002710205	76.8109	95	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720115.1	s__MGIIa-K1 sp002720115	76.6021	51	445	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:13:10,327] [INFO] GTDB search result was written to OceanDNA-a1938/result_gtdb.tsv
[2023-03-16 01:13:10,327] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:13:10,328] [INFO] DFAST_QC result json was written to OceanDNA-a1938/dqc_result.json
[2023-03-16 01:13:10,328] [INFO] DFAST_QC completed!
[2023-03-16 01:13:10,328] [INFO] Total running time: 0h0m41s