[2023-03-17 02:18:53,703] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:18:53,703] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:18:53,704] [INFO] DQC Reference Directory: /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference
[2023-03-17 02:18:54,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:18:54,826] [INFO] Task started: Prodigal
[2023-03-17 02:18:54,826] [INFO] Running command: cat /var/lib/cwl/stg2189ba78-83f6-4bb3-bccc-a4ceb01f3bb1/OceanDNA-b37510.fa | prodigal -d OceanDNA-b37510/cds.fna -a OceanDNA-b37510/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:19:12,671] [INFO] Task succeeded: Prodigal
[2023-03-17 02:19:12,671] [INFO] Task started: HMMsearch
[2023-03-17 02:19:12,671] [INFO] Running command: hmmsearch --tblout OceanDNA-b37510/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/reference_markers.hmm OceanDNA-b37510/protein.faa > /dev/null
[2023-03-17 02:19:12,859] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:19:12,860] [INFO] Found 6/6 markers.
[2023-03-17 02:19:12,879] [INFO] Query marker FASTA was written to OceanDNA-b37510/markers.fasta
[2023-03-17 02:19:12,880] [INFO] Task started: Blastn
[2023-03-17 02:19:12,880] [INFO] Running command: blastn -query OceanDNA-b37510/markers.fasta -db /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/reference_markers.fasta -out OceanDNA-b37510/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:19:13,554] [INFO] Task succeeded: Blastn
[2023-03-17 02:19:13,555] [INFO] Selected 24 target genomes.
[2023-03-17 02:19:13,555] [INFO] Target genome list was writen to OceanDNA-b37510/target_genomes.txt
[2023-03-17 02:19:13,570] [INFO] Task started: fastANI
[2023-03-17 02:19:13,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg2189ba78-83f6-4bb3-bccc-a4ceb01f3bb1/OceanDNA-b37510.fa --refList OceanDNA-b37510/target_genomes.txt --output OceanDNA-b37510/fastani_result.tsv --threads 1
[2023-03-17 02:19:27,662] [INFO] Task succeeded: fastANI
[2023-03-17 02:19:27,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:19:27,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:19:27,669] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 02:19:27,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 02:19:27,670] [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
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	98.5733	938	963	95	conclusive
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.4403	152	963	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	77.4399	150	963	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.3652	154	963	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.315	163	963	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.1334	152	963	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.1082	146	963	95	below_threshold
Sediminihaliea albiluteola	strain=F7430	GCA_014077625.1	2758564	2758564	type	True	76.9383	74	963	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	76.8793	171	963	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.8432	202	963	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.6435	117	963	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:19:27,670] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37510/tc_result.tsv
[2023-03-17 02:19:27,670] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:19:27,670] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:19:27,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/checkm_data
[2023-03-17 02:19:27,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:19:27,675] [INFO] Task started: CheckM
[2023-03-17 02:19:27,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37510/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37510/checkm_input OceanDNA-b37510/checkm_result
[2023-03-17 02:20:14,056] [INFO] Task succeeded: CheckM
[2023-03-17 02:20:14,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:20:14,059] [INFO] ===== Completeness check finished =====
[2023-03-17 02:20:14,059] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:20:14,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37510/markers.fasta)
[2023-03-17 02:20:14,061] [INFO] Task started: Blastn
[2023-03-17 02:20:14,061] [INFO] Running command: blastn -query OceanDNA-b37510/markers.fasta -db /var/lib/cwl/stga366d3f3-d5c3-429c-90a0-30ca47cbd0d3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37510/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:20:15,253] [INFO] Task succeeded: Blastn
[2023-03-17 02:20:15,254] [INFO] Selected 21 target genomes.
[2023-03-17 02:20:15,254] [INFO] Target genome list was writen to OceanDNA-b37510/target_genomes_gtdb.txt
[2023-03-17 02:20:15,699] [INFO] Task started: fastANI
[2023-03-17 02:20:15,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg2189ba78-83f6-4bb3-bccc-a4ceb01f3bb1/OceanDNA-b37510.fa --refList OceanDNA-b37510/target_genomes_gtdb.txt --output OceanDNA-b37510/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:20:28,156] [INFO] Task succeeded: fastANI
[2023-03-17 02:20:28,164] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:20:28,164] [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
GCF_014652275.1	s__Halioglobus_A pacificus	98.5733	938	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus_A	95.0	98.67	98.67	0.96	0.96	2	conclusive
GCF_001983995.1	s__Halioglobus japonicus	77.3652	154	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008064635.1	s__Parahaliea aestuarii	77.3326	162	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.1083	146	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.0932	167	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.0781	120	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.0163	139	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	76.8793	171	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.8425	201	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.7463	146	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340525.1	s__Chromatocurvus halotolerans	76.6596	85	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Chromatocurvus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003719295.1	s__Haliea alexandrii	76.6255	118	963	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:20:28,164] [INFO] GTDB search result was written to OceanDNA-b37510/result_gtdb.tsv
[2023-03-17 02:20:28,164] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:20:28,166] [INFO] DFAST_QC result json was written to OceanDNA-b37510/dqc_result.json
[2023-03-17 02:20:28,166] [INFO] DFAST_QC completed!
[2023-03-17 02:20:28,166] [INFO] Total running time: 0h1m34s