[2023-03-17 06:30:49,085] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,086] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference
[2023-03-17 06:30:50,271] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stgb18017a0-6940-40a8-817c-0b05f032991b/OceanDNA-b3697.fa | prodigal -d OceanDNA-b3697/cds.fna -a OceanDNA-b3697/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:31:07,305] [INFO] Task succeeded: Prodigal
[2023-03-17 06:31:07,305] [INFO] Task started: HMMsearch
[2023-03-17 06:31:07,305] [INFO] Running command: hmmsearch --tblout OceanDNA-b3697/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/reference_markers.hmm OceanDNA-b3697/protein.faa > /dev/null
[2023-03-17 06:31:07,503] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:31:07,504] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgb18017a0-6940-40a8-817c-0b05f032991b/OceanDNA-b3697.fa]
[2023-03-17 06:31:07,526] [INFO] Query marker FASTA was written to OceanDNA-b3697/markers.fasta
[2023-03-17 06:31:07,526] [INFO] Task started: Blastn
[2023-03-17 06:31:07,526] [INFO] Running command: blastn -query OceanDNA-b3697/markers.fasta -db /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/reference_markers.fasta -out OceanDNA-b3697/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:07,996] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:07,996] [INFO] Selected 15 target genomes.
[2023-03-17 06:31:07,997] [INFO] Target genome list was writen to OceanDNA-b3697/target_genomes.txt
[2023-03-17 06:31:08,005] [INFO] Task started: fastANI
[2023-03-17 06:31:08,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgb18017a0-6940-40a8-817c-0b05f032991b/OceanDNA-b3697.fa --refList OceanDNA-b3697/target_genomes.txt --output OceanDNA-b3697/fastani_result.tsv --threads 1
[2023-03-17 06:31:20,896] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:20,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:20,896] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:20,901] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:20,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 06:31:20,901] [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
Neolewinella antarctica	strain=DSM 105096	GCA_011927835.1	442734	442734	type	True	77.2055	90	481	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	76.8149	88	481	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	76.1486	81	481	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 06:31:20,901] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3697/tc_result.tsv
[2023-03-17 06:31:20,901] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:20,901] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:20,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/checkm_data
[2023-03-17 06:31:20,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:20,907] [INFO] Task started: CheckM
[2023-03-17 06:31:20,907] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3697/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3697/checkm_input OceanDNA-b3697/checkm_result
[2023-03-17 06:32:06,325] [INFO] Task succeeded: CheckM
[2023-03-17 06:32:06,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:32:06,328] [INFO] ===== Completeness check finished =====
[2023-03-17 06:32:06,328] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:32:06,328] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3697/markers.fasta)
[2023-03-17 06:32:06,328] [INFO] Task started: Blastn
[2023-03-17 06:32:06,329] [INFO] Running command: blastn -query OceanDNA-b3697/markers.fasta -db /var/lib/cwl/stg50350a0f-8d3a-4c13-823a-79aab97510e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3697/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:32:06,849] [INFO] Task succeeded: Blastn
[2023-03-17 06:32:06,850] [INFO] Selected 12 target genomes.
[2023-03-17 06:32:06,850] [INFO] Target genome list was writen to OceanDNA-b3697/target_genomes_gtdb.txt
[2023-03-17 06:32:07,015] [INFO] Task started: fastANI
[2023-03-17 06:32:07,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgb18017a0-6940-40a8-817c-0b05f032991b/OceanDNA-b3697.fa --refList OceanDNA-b3697/target_genomes_gtdb.txt --output OceanDNA-b3697/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:32:15,317] [INFO] Task succeeded: fastANI
[2023-03-17 06:32:15,322] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:32:15,323] [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_011927835.1	s__Lewinella_A antarctica	77.2055	90	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	77.1003	117	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004375085.3	s__Lewinella_A sp004375085	77.0532	78	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	77.0191	106	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390915.1	s__Lewinella_A sp003390915	77.0135	112	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625015.1	s__Lewinella_A sp001625015	76.9808	116	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934605.1	s__Lewinella_A xylanilytica	76.1314	82	481	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:32:15,323] [INFO] GTDB search result was written to OceanDNA-b3697/result_gtdb.tsv
[2023-03-17 06:32:15,323] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:32:15,324] [INFO] DFAST_QC result json was written to OceanDNA-b3697/dqc_result.json
[2023-03-17 06:32:15,324] [INFO] DFAST_QC completed!
[2023-03-17 06:32:15,324] [INFO] Total running time: 0h1m26s