[2023-03-16 17:14:20,580] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:14:20,581] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:14:20,581] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference
[2023-03-16 17:14:21,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:14:21,955] [INFO] Task started: Prodigal
[2023-03-16 17:14:21,955] [INFO] Running command: cat /var/lib/cwl/stgf2ba3167-b1ca-4420-82b1-8d9e05386953/OceanDNA-b10396.fa | prodigal -d OceanDNA-b10396/cds.fna -a OceanDNA-b10396/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:14:27,804] [INFO] Task succeeded: Prodigal
[2023-03-16 17:14:27,804] [INFO] Task started: HMMsearch
[2023-03-16 17:14:27,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b10396/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/reference_markers.hmm OceanDNA-b10396/protein.faa > /dev/null
[2023-03-16 17:14:27,982] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:14:27,982] [INFO] Found 6/6 markers.
[2023-03-16 17:14:27,994] [INFO] Query marker FASTA was written to OceanDNA-b10396/markers.fasta
[2023-03-16 17:14:27,996] [INFO] Task started: Blastn
[2023-03-16 17:14:27,996] [INFO] Running command: blastn -query OceanDNA-b10396/markers.fasta -db /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/reference_markers.fasta -out OceanDNA-b10396/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:14:28,624] [INFO] Task succeeded: Blastn
[2023-03-16 17:14:28,625] [INFO] Selected 26 target genomes.
[2023-03-16 17:14:28,625] [INFO] Target genome list was writen to OceanDNA-b10396/target_genomes.txt
[2023-03-16 17:14:28,654] [INFO] Task started: fastANI
[2023-03-16 17:14:28,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ba3167-b1ca-4420-82b1-8d9e05386953/OceanDNA-b10396.fa --refList OceanDNA-b10396/target_genomes.txt --output OceanDNA-b10396/fastani_result.tsv --threads 1
[2023-03-16 17:14:49,778] [INFO] Task succeeded: fastANI
[2023-03-16 17:14:49,779] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:14:49,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:14:49,779] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:14:49,779] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:14:49,779] [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
--------------------------------------------------------------------------------
[2023-03-16 17:14:49,779] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10396/tc_result.tsv
[2023-03-16 17:14:49,780] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:14:49,780] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:14:49,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/checkm_data
[2023-03-16 17:14:49,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:14:50,185] [INFO] Task started: CheckM
[2023-03-16 17:14:50,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10396/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10396/checkm_input OceanDNA-b10396/checkm_result
[2023-03-16 17:15:15,515] [INFO] Task succeeded: CheckM
[2023-03-16 17:15:15,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:15:15,517] [INFO] ===== Completeness check finished =====
[2023-03-16 17:15:15,517] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:15:15,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10396/markers.fasta)
[2023-03-16 17:15:15,518] [INFO] Task started: Blastn
[2023-03-16 17:15:15,518] [INFO] Running command: blastn -query OceanDNA-b10396/markers.fasta -db /var/lib/cwl/stgb5861007-55e3-4f70-8df5-0e1ffbfc6e1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10396/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:15:16,630] [INFO] Task succeeded: Blastn
[2023-03-16 17:15:16,631] [INFO] Selected 12 target genomes.
[2023-03-16 17:15:16,631] [INFO] Target genome list was writen to OceanDNA-b10396/target_genomes_gtdb.txt
[2023-03-16 17:15:16,688] [INFO] Task started: fastANI
[2023-03-16 17:15:16,688] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2ba3167-b1ca-4420-82b1-8d9e05386953/OceanDNA-b10396.fa --refList OceanDNA-b10396/target_genomes_gtdb.txt --output OceanDNA-b10396/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:15:20,305] [INFO] Task succeeded: fastANI
[2023-03-16 17:15:20,311] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:15:20,311] [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_902593075.1	s__TMED96 sp902593075	85.8229	156	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171475.2	s__TMED96 sp002171475	84.679	186	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	99.27	99.27	0.93	0.93	2	-
GCA_902598305.1	s__TMED96 sp902598305	84.6506	196	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628605.1	s__TMED96 sp902628605	84.3258	101	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728075.1	s__TMED96 sp002728075	84.1943	167	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595825.1	s__TMED96 sp902595825	83.8388	140	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635965.1	s__TMED96 sp902635965	83.272	179	225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED96	95.0	97.75	95.54	0.87	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-16 17:15:20,311] [INFO] GTDB search result was written to OceanDNA-b10396/result_gtdb.tsv
[2023-03-16 17:15:20,311] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:15:20,312] [INFO] DFAST_QC result json was written to OceanDNA-b10396/dqc_result.json
[2023-03-16 17:15:20,312] [INFO] DFAST_QC completed!
[2023-03-16 17:15:20,312] [INFO] Total running time: 0h0m60s