[2023-03-18 23:48:46,606] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:48:46,606] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:48:46,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference
[2023-03-18 23:48:47,724] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:48:47,725] [INFO] Task started: Prodigal
[2023-03-18 23:48:47,725] [INFO] Running command: cat /var/lib/cwl/stg786b112b-76dd-415a-b486-38271d584f46/OceanDNA-b16161.fa | prodigal -d OceanDNA-b16161/cds.fna -a OceanDNA-b16161/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:49:10,178] [INFO] Task succeeded: Prodigal
[2023-03-18 23:49:10,178] [INFO] Task started: HMMsearch
[2023-03-18 23:49:10,178] [INFO] Running command: hmmsearch --tblout OceanDNA-b16161/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/reference_markers.hmm OceanDNA-b16161/protein.faa > /dev/null
[2023-03-18 23:49:10,386] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:49:10,386] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg786b112b-76dd-415a-b486-38271d584f46/OceanDNA-b16161.fa]
[2023-03-18 23:49:10,412] [INFO] Query marker FASTA was written to OceanDNA-b16161/markers.fasta
[2023-03-18 23:49:10,413] [INFO] Task started: Blastn
[2023-03-18 23:49:10,413] [INFO] Running command: blastn -query OceanDNA-b16161/markers.fasta -db /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/reference_markers.fasta -out OceanDNA-b16161/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:49:10,849] [INFO] Task succeeded: Blastn
[2023-03-18 23:49:10,850] [INFO] Selected 9 target genomes.
[2023-03-18 23:49:10,850] [INFO] Target genome list was writen to OceanDNA-b16161/target_genomes.txt
[2023-03-18 23:49:10,866] [INFO] Task started: fastANI
[2023-03-18 23:49:10,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg786b112b-76dd-415a-b486-38271d584f46/OceanDNA-b16161.fa --refList OceanDNA-b16161/target_genomes.txt --output OceanDNA-b16161/fastani_result.tsv --threads 1
[2023-03-18 23:49:18,139] [INFO] Task succeeded: fastANI
[2023-03-18 23:49:18,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:49:18,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:49:18,144] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:49:18,144] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:49:18,144] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	76.2042	160	1213	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	76.1251	201	1213	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:49:18,144] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16161/tc_result.tsv
[2023-03-18 23:49:18,144] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:49:18,144] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:49:18,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/checkm_data
[2023-03-18 23:49:18,146] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:49:18,153] [INFO] Task started: CheckM
[2023-03-18 23:49:18,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16161/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16161/checkm_input OceanDNA-b16161/checkm_result
[2023-03-18 23:50:15,071] [INFO] Task succeeded: CheckM
[2023-03-18 23:50:15,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 14.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 23:50:15,123] [INFO] ===== Completeness check finished =====
[2023-03-18 23:50:15,123] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:50:15,123] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16161/markers.fasta)
[2023-03-18 23:50:15,124] [INFO] Task started: Blastn
[2023-03-18 23:50:15,125] [INFO] Running command: blastn -query OceanDNA-b16161/markers.fasta -db /var/lib/cwl/stg0ee8f843-8ca0-4be7-a89a-d7f10b0f0643/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16161/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:50:15,560] [INFO] Task succeeded: Blastn
[2023-03-18 23:50:15,560] [INFO] Selected 14 target genomes.
[2023-03-18 23:50:15,561] [INFO] Target genome list was writen to OceanDNA-b16161/target_genomes_gtdb.txt
[2023-03-18 23:50:15,577] [INFO] Task started: fastANI
[2023-03-18 23:50:15,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg786b112b-76dd-415a-b486-38271d584f46/OceanDNA-b16161.fa --refList OceanDNA-b16161/target_genomes_gtdb.txt --output OceanDNA-b16161/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:50:29,328] [INFO] Task succeeded: fastANI
[2023-03-18 23:50:29,334] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:50:29,334] [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_900659865.1	s__Hyella patelloides	79.0189	620	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	77.6652	474	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	76.2056	168	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	76.1333	200	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207195.1	s__Pleurocapsa sp015207195	76.1229	172	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.9967	184	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332055.1	s__Xenococcus sp000332055	75.9742	131	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Xenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	75.9513	131	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756305.1	s__Myxosarcina sp000756305	75.9076	189	1213	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Myxosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:50:29,337] [INFO] GTDB search result was written to OceanDNA-b16161/result_gtdb.tsv
[2023-03-18 23:50:29,338] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:50:29,339] [INFO] DFAST_QC result json was written to OceanDNA-b16161/dqc_result.json
[2023-03-18 23:50:29,339] [INFO] DFAST_QC completed!
[2023-03-18 23:50:29,339] [INFO] Total running time: 0h1m43s