[2023-03-19 01:13:44,407] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,407] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,407] [INFO] DQC Reference Directory: /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference
[2023-03-19 01:13:45,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,675] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,675] [INFO] Running command: cat /var/lib/cwl/stga74789a9-169e-4f0e-9290-0051b5723b00/OceanDNA-a3994.fa | prodigal -d OceanDNA-a3994/cds.fna -a OceanDNA-a3994/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:13:53,217] [INFO] Task succeeded: Prodigal
[2023-03-19 01:13:53,217] [INFO] Task started: HMMsearch
[2023-03-19 01:13:53,217] [INFO] Running command: hmmsearch --tblout OceanDNA-a3994/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/reference_markers.hmm OceanDNA-a3994/protein.faa > /dev/null
[2023-03-19 01:13:53,389] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:13:53,389] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga74789a9-169e-4f0e-9290-0051b5723b00/OceanDNA-a3994.fa]
[2023-03-19 01:13:53,399] [INFO] Query marker FASTA was written to OceanDNA-a3994/markers.fasta
[2023-03-19 01:13:53,399] [INFO] Task started: Blastn
[2023-03-19 01:13:53,399] [INFO] Running command: blastn -query OceanDNA-a3994/markers.fasta -db /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/reference_markers.fasta -out OceanDNA-a3994/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:13:53,829] [INFO] Task succeeded: Blastn
[2023-03-19 01:13:53,829] [INFO] Selected 2 target genomes.
[2023-03-19 01:13:53,830] [INFO] Target genome list was writen to OceanDNA-a3994/target_genomes.txt
[2023-03-19 01:13:53,831] [INFO] Task started: fastANI
[2023-03-19 01:13:53,831] [INFO] Running command: fastANI --query /var/lib/cwl/stga74789a9-169e-4f0e-9290-0051b5723b00/OceanDNA-a3994.fa --refList OceanDNA-a3994/target_genomes.txt --output OceanDNA-a3994/fastani_result.tsv --threads 1
[2023-03-19 01:13:54,641] [INFO] Task succeeded: fastANI
[2023-03-19 01:13:54,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:13:54,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:13:54,641] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:13:54,641] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:13:54,641] [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
--------------------------------------------------------------------------------
[2023-03-19 01:13:54,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3994/tc_result.tsv
[2023-03-19 01:13:54,642] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:13:54,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:13:54,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/checkm_data
[2023-03-19 01:13:54,644] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:13:54,822] [INFO] Task started: CheckM
[2023-03-19 01:13:54,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3994/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3994/checkm_input OceanDNA-a3994/checkm_result
[2023-03-19 01:14:18,702] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:18,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:18,708] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:18,708] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:18,709] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3994/markers.fasta)
[2023-03-19 01:14:18,710] [INFO] Task started: Blastn
[2023-03-19 01:14:18,710] [INFO] Running command: blastn -query OceanDNA-a3994/markers.fasta -db /var/lib/cwl/stge50e4117-3fdb-42a2-85af-824c85fffcbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3994/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:19,138] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:19,139] [INFO] Selected 8 target genomes.
[2023-03-19 01:14:19,139] [INFO] Target genome list was writen to OceanDNA-a3994/target_genomes_gtdb.txt
[2023-03-19 01:14:19,149] [INFO] Task started: fastANI
[2023-03-19 01:14:19,149] [INFO] Running command: fastANI --query /var/lib/cwl/stga74789a9-169e-4f0e-9290-0051b5723b00/OceanDNA-a3994.fa --refList OceanDNA-a3994/target_genomes_gtdb.txt --output OceanDNA-a3994/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:14:21,507] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:21,512] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:14:21,513] [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_002504905.1	s__MGIIb-O2 sp002504905	99.8186	444	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	99.85	99.68	0.95	0.91	6	conclusive
GCA_002497245.1	s__MGIIb-O2 sp002497245	83.4551	385	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.50	97.50	0.90	0.90	2	-
GCA_902593945.1	s__MGIIb-O2 sp902593945	83.4547	325	463	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_002498985.1	s__MGIIb-O2 sp002498985	81.9105	310	463	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_002685315.1	s__MGIIb-O2 sp002685315	81.3965	229	463	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_002686525.1	s__MGIIb-O2 sp002686525	79.7721	281	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	97.02	96.68	0.82	0.74	10	-
GCA_002494975.1	s__MGIIb-O2 sp002494975	78.207	163	463	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O2	95.0	98.81	97.76	0.81	0.69	24	-
--------------------------------------------------------------------------------
[2023-03-19 01:14:21,513] [INFO] GTDB search result was written to OceanDNA-a3994/result_gtdb.tsv
[2023-03-19 01:14:21,513] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:14:21,514] [INFO] DFAST_QC result json was written to OceanDNA-a3994/dqc_result.json
[2023-03-19 01:14:21,514] [INFO] DFAST_QC completed!
[2023-03-19 01:14:21,514] [INFO] Total running time: 0h0m37s