[2023-03-18 20:40:39,435] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference
[2023-03-18 20:40:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stgd7ffa324-887c-463f-a884-305a655561ff/OceanDNA-b3678.fa | prodigal -d OceanDNA-b3678/cds.fna -a OceanDNA-b3678/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:41:06,973] [INFO] Task succeeded: Prodigal
[2023-03-18 20:41:06,974] [INFO] Task started: HMMsearch
[2023-03-18 20:41:06,974] [INFO] Running command: hmmsearch --tblout OceanDNA-b3678/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/reference_markers.hmm OceanDNA-b3678/protein.faa > /dev/null
[2023-03-18 20:41:07,178] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:41:07,179] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd7ffa324-887c-463f-a884-305a655561ff/OceanDNA-b3678.fa]
[2023-03-18 20:41:07,205] [INFO] Query marker FASTA was written to OceanDNA-b3678/markers.fasta
[2023-03-18 20:41:07,205] [INFO] Task started: Blastn
[2023-03-18 20:41:07,205] [INFO] Running command: blastn -query OceanDNA-b3678/markers.fasta -db /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/reference_markers.fasta -out OceanDNA-b3678/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:07,665] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:07,666] [INFO] Selected 10 target genomes.
[2023-03-18 20:41:07,666] [INFO] Target genome list was writen to OceanDNA-b3678/target_genomes.txt
[2023-03-18 20:41:07,670] [INFO] Task started: fastANI
[2023-03-18 20:41:07,671] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ffa324-887c-463f-a884-305a655561ff/OceanDNA-b3678.fa --refList OceanDNA-b3678/target_genomes.txt --output OceanDNA-b3678/fastani_result.tsv --threads 1
[2023-03-18 20:41:14,296] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:14,297] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:14,297] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:14,300] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:14,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:14,300] [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
Cellulomonas carbonis	strain=T26	GCA_000767175.1	1386092	1386092	type	True	74.6855	121	1018	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:14,300] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3678/tc_result.tsv
[2023-03-18 20:41:14,300] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:14,300] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:14,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/checkm_data
[2023-03-18 20:41:14,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:14,307] [INFO] Task started: CheckM
[2023-03-18 20:41:14,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3678/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3678/checkm_input OceanDNA-b3678/checkm_result
[2023-03-18 20:42:15,654] [INFO] Task succeeded: CheckM
[2023-03-18 20:42:15,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 48.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:42:15,657] [INFO] ===== Completeness check finished =====
[2023-03-18 20:42:15,657] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:42:15,657] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3678/markers.fasta)
[2023-03-18 20:42:15,657] [INFO] Task started: Blastn
[2023-03-18 20:42:15,657] [INFO] Running command: blastn -query OceanDNA-b3678/markers.fasta -db /var/lib/cwl/stgd12c95d2-98a3-4cf6-9c4f-4fcc6f861a43/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3678/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:42:16,171] [INFO] Task succeeded: Blastn
[2023-03-18 20:42:16,172] [INFO] Selected 9 target genomes.
[2023-03-18 20:42:16,172] [INFO] Target genome list was writen to OceanDNA-b3678/target_genomes_gtdb.txt
[2023-03-18 20:42:16,181] [INFO] Task started: fastANI
[2023-03-18 20:42:16,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ffa324-887c-463f-a884-305a655561ff/OceanDNA-b3678.fa --refList OceanDNA-b3678/target_genomes_gtdb.txt --output OceanDNA-b3678/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:42:21,335] [INFO] Task succeeded: fastANI
[2023-03-18 20:42:21,338] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:42:21,338] [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_018267055.1	s__PHOS-HE28 sp018267055	75.2117	54	1018	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:42:21,338] [INFO] GTDB search result was written to OceanDNA-b3678/result_gtdb.tsv
[2023-03-18 20:42:21,338] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:42:21,338] [INFO] DFAST_QC result json was written to OceanDNA-b3678/dqc_result.json
[2023-03-18 20:42:21,339] [INFO] DFAST_QC completed!
[2023-03-18 20:42:21,339] [INFO] Total running time: 0h1m42s