[2023-03-15 10:49:28,632] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:49:28,632] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:49:28,632] [INFO] DQC Reference Directory: /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference
[2023-03-15 10:49:29,763] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:49:29,764] [INFO] Task started: Prodigal
[2023-03-15 10:49:29,764] [INFO] Running command: cat /var/lib/cwl/stgc7345a71-84bf-45f0-8778-43f3f072fc3b/OceanDNA-b14516.fa | prodigal -d OceanDNA-b14516/cds.fna -a OceanDNA-b14516/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:49:40,128] [INFO] Task succeeded: Prodigal
[2023-03-15 10:49:40,129] [INFO] Task started: HMMsearch
[2023-03-15 10:49:40,129] [INFO] Running command: hmmsearch --tblout OceanDNA-b14516/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/reference_markers.hmm OceanDNA-b14516/protein.faa > /dev/null
[2023-03-15 10:49:40,298] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:49:40,298] [INFO] Found 6/6 markers.
[2023-03-15 10:49:40,312] [INFO] Query marker FASTA was written to OceanDNA-b14516/markers.fasta
[2023-03-15 10:49:40,312] [INFO] Task started: Blastn
[2023-03-15 10:49:40,312] [INFO] Running command: blastn -query OceanDNA-b14516/markers.fasta -db /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/reference_markers.fasta -out OceanDNA-b14516/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:49:40,864] [INFO] Task succeeded: Blastn
[2023-03-15 10:49:40,865] [INFO] Selected 3 target genomes.
[2023-03-15 10:49:40,865] [INFO] Target genome list was writen to OceanDNA-b14516/target_genomes.txt
[2023-03-15 10:49:40,867] [INFO] Task started: fastANI
[2023-03-15 10:49:40,867] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7345a71-84bf-45f0-8778-43f3f072fc3b/OceanDNA-b14516.fa --refList OceanDNA-b14516/target_genomes.txt --output OceanDNA-b14516/fastani_result.tsv --threads 1
[2023-03-15 10:49:42,553] [INFO] Task succeeded: fastANI
[2023-03-15 10:49:42,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:49:42,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:49:42,554] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:49:42,554] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 10:49:42,554] [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
--------------------------------------------------------------------------------
[2023-03-15 10:49:42,554] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14516/tc_result.tsv
[2023-03-15 10:49:42,554] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:49:42,554] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:49:42,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/checkm_data
[2023-03-15 10:49:42,558] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:49:42,561] [INFO] Task started: CheckM
[2023-03-15 10:49:42,562] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14516/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14516/checkm_input OceanDNA-b14516/checkm_result
[2023-03-15 10:50:13,569] [INFO] Task succeeded: CheckM
[2023-03-15 10:50:13,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:50:13,572] [INFO] ===== Completeness check finished =====
[2023-03-15 10:50:13,572] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:50:13,572] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14516/markers.fasta)
[2023-03-15 10:50:13,572] [INFO] Task started: Blastn
[2023-03-15 10:50:13,572] [INFO] Running command: blastn -query OceanDNA-b14516/markers.fasta -db /var/lib/cwl/stge27a062e-7043-4c6a-bf54-c3c1d488da15/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14516/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:50:14,292] [INFO] Task succeeded: Blastn
[2023-03-15 10:50:14,294] [INFO] Selected 11 target genomes.
[2023-03-15 10:50:14,294] [INFO] Target genome list was writen to OceanDNA-b14516/target_genomes_gtdb.txt
[2023-03-15 10:50:14,308] [INFO] Task started: fastANI
[2023-03-15 10:50:14,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7345a71-84bf-45f0-8778-43f3f072fc3b/OceanDNA-b14516.fa --refList OceanDNA-b14516/target_genomes_gtdb.txt --output OceanDNA-b14516/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:50:18,335] [INFO] Task succeeded: fastANI
[2023-03-15 10:50:18,339] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-15 10:50:18,339] [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_003509065.1	s__UBA8106 sp003509065	95.4119	85	601	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA823;g__UBA8106	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002725925.1	s__GCA-002725925 sp002725925	95.2792	364	601	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002687335.1	s__GCA-002725925 sp002687335	84.9368	237	601	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008373165.1	s__GCA-002725925 sp009392785	84.0202	443	601	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	98.70	97.00	0.83	0.72	6	-
GCA_009392215.1	s__GCA-002725925 sp009392215	82.6213	414	601	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__GCA-002725925	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:50:18,339] [INFO] GTDB search result was written to OceanDNA-b14516/result_gtdb.tsv
[2023-03-15 10:50:18,339] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:50:18,340] [INFO] DFAST_QC result json was written to OceanDNA-b14516/dqc_result.json
[2023-03-15 10:50:18,340] [INFO] DFAST_QC completed!
[2023-03-15 10:50:18,340] [INFO] Total running time: 0h0m50s