[2023-03-15 12:44:24,470] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,470] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,470] [INFO] DQC Reference Directory: /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference
[2023-03-15 12:44:26,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,207] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,207] [INFO] Running command: cat /var/lib/cwl/stg1133089f-2da0-4f48-a022-546a0a2227b9/OceanDNA-b16109.fa | prodigal -d OceanDNA-b16109/cds.fna -a OceanDNA-b16109/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:47,251] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:47,251] [INFO] Task started: HMMsearch
[2023-03-15 12:44:47,251] [INFO] Running command: hmmsearch --tblout OceanDNA-b16109/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/reference_markers.hmm OceanDNA-b16109/protein.faa > /dev/null
[2023-03-15 12:44:47,529] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:47,530] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1133089f-2da0-4f48-a022-546a0a2227b9/OceanDNA-b16109.fa]
[2023-03-15 12:44:47,570] [INFO] Query marker FASTA was written to OceanDNA-b16109/markers.fasta
[2023-03-15 12:44:47,570] [INFO] Task started: Blastn
[2023-03-15 12:44:47,570] [INFO] Running command: blastn -query OceanDNA-b16109/markers.fasta -db /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/reference_markers.fasta -out OceanDNA-b16109/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:48,089] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:48,090] [INFO] Selected 12 target genomes.
[2023-03-15 12:44:48,090] [INFO] Target genome list was writen to OceanDNA-b16109/target_genomes.txt
[2023-03-15 12:44:48,097] [INFO] Task started: fastANI
[2023-03-15 12:44:48,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg1133089f-2da0-4f48-a022-546a0a2227b9/OceanDNA-b16109.fa --refList OceanDNA-b16109/target_genomes.txt --output OceanDNA-b16109/fastani_result.tsv --threads 1
[2023-03-15 12:44:59,155] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:59,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:59,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:59,156] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:59,156] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:59,156] [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 12:44:59,156] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16109/tc_result.tsv
[2023-03-15 12:44:59,158] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:59,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:59,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/checkm_data
[2023-03-15 12:44:59,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:59,177] [INFO] Task started: CheckM
[2023-03-15 12:44:59,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16109/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16109/checkm_input OceanDNA-b16109/checkm_result
[2023-03-15 12:45:52,325] [INFO] Task succeeded: CheckM
[2023-03-15 12:45:52,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.03%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 12:45:52,330] [INFO] ===== Completeness check finished =====
[2023-03-15 12:45:52,330] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:45:52,330] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16109/markers.fasta)
[2023-03-15 12:45:52,331] [INFO] Task started: Blastn
[2023-03-15 12:45:52,331] [INFO] Running command: blastn -query OceanDNA-b16109/markers.fasta -db /var/lib/cwl/stgcca9abfb-9bf6-4d36-a4b7-7d3a964cc521/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16109/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:45:53,038] [INFO] Task succeeded: Blastn
[2023-03-15 12:45:53,039] [INFO] Selected 17 target genomes.
[2023-03-15 12:45:53,039] [INFO] Target genome list was writen to OceanDNA-b16109/target_genomes_gtdb.txt
[2023-03-15 12:45:53,144] [INFO] Task started: fastANI
[2023-03-15 12:45:53,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg1133089f-2da0-4f48-a022-546a0a2227b9/OceanDNA-b16109.fa --refList OceanDNA-b16109/target_genomes_gtdb.txt --output OceanDNA-b16109/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:46:12,214] [INFO] Task succeeded: fastANI
[2023-03-15 12:46:12,218] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:46:12,218] [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_010672965.1	s__SIO1A7 sp010672965	92.644	998	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__SIO1A7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446395.1	s__DSPX01 sp016446395	75.6742	73	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__DSPX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390955.1	s__Planktothricoides sp011390955	75.534	77	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276715.1	s__Planktothricoides sp001276715	75.448	66	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Planktothricoides	95.0	99.30	99.29	0.94	0.94	3	-
GCF_014696265.1	s__FACHB-1375 sp014696265	75.1949	58	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Phormidiaceae_A;g__FACHB-1375	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317475.1	s__Microcoleus sp000317475	74.774	51	1114	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:46:12,219] [INFO] GTDB search result was written to OceanDNA-b16109/result_gtdb.tsv
[2023-03-15 12:46:12,219] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:46:12,220] [INFO] DFAST_QC result json was written to OceanDNA-b16109/dqc_result.json
[2023-03-15 12:46:12,220] [INFO] DFAST_QC completed!
[2023-03-15 12:46:12,220] [INFO] Total running time: 0h1m48s