[2023-03-19 00:33:18,972] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:18,972] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:18,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference
[2023-03-19 00:33:20,252] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,253] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,253] [INFO] Running command: cat /var/lib/cwl/stg9f0cac30-6502-48f2-8a13-c739a27c6955/OceanDNA-b5611.fa | prodigal -d OceanDNA-b5611/cds.fna -a OceanDNA-b5611/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:52,305] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:52,305] [INFO] Task started: HMMsearch
[2023-03-19 00:33:52,305] [INFO] Running command: hmmsearch --tblout OceanDNA-b5611/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/reference_markers.hmm OceanDNA-b5611/protein.faa > /dev/null
[2023-03-19 00:33:52,574] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:52,575] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9f0cac30-6502-48f2-8a13-c739a27c6955/OceanDNA-b5611.fa]
[2023-03-19 00:33:52,604] [INFO] Query marker FASTA was written to OceanDNA-b5611/markers.fasta
[2023-03-19 00:33:52,605] [INFO] Task started: Blastn
[2023-03-19 00:33:52,605] [INFO] Running command: blastn -query OceanDNA-b5611/markers.fasta -db /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/reference_markers.fasta -out OceanDNA-b5611/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:53,146] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:53,149] [INFO] Selected 23 target genomes.
[2023-03-19 00:33:53,149] [INFO] Target genome list was writen to OceanDNA-b5611/target_genomes.txt
[2023-03-19 00:33:53,169] [INFO] Task started: fastANI
[2023-03-19 00:33:53,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0cac30-6502-48f2-8a13-c739a27c6955/OceanDNA-b5611.fa --refList OceanDNA-b5611/target_genomes.txt --output OceanDNA-b5611/fastani_result.tsv --threads 1
[2023-03-19 00:34:07,048] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:07,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:34:07,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:34:07,052] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:34:07,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:34:07,052] [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
Owenweeksia hongkongensis	strain=DSM 17368	GCA_000236705.1	253245	253245	type	True	75.9785	71	1391	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:34:07,054] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5611/tc_result.tsv
[2023-03-19 00:34:07,054] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:34:07,054] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:34:07,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/checkm_data
[2023-03-19 00:34:07,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:34:07,061] [INFO] Task started: CheckM
[2023-03-19 00:34:07,061] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5611/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5611/checkm_input OceanDNA-b5611/checkm_result
[2023-03-19 00:35:25,409] [INFO] Task succeeded: CheckM
[2023-03-19 00:35:25,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:35:25,417] [INFO] ===== Completeness check finished =====
[2023-03-19 00:35:25,417] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:35:25,417] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5611/markers.fasta)
[2023-03-19 00:35:25,418] [INFO] Task started: Blastn
[2023-03-19 00:35:25,418] [INFO] Running command: blastn -query OceanDNA-b5611/markers.fasta -db /var/lib/cwl/stgf1c27f9b-dc9e-43cc-88b0-9f34132f9190/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5611/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:35:26,094] [INFO] Task succeeded: Blastn
[2023-03-19 00:35:26,097] [INFO] Selected 24 target genomes.
[2023-03-19 00:35:26,097] [INFO] Target genome list was writen to OceanDNA-b5611/target_genomes_gtdb.txt
[2023-03-19 00:35:26,134] [INFO] Task started: fastANI
[2023-03-19 00:35:26,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f0cac30-6502-48f2-8a13-c739a27c6955/OceanDNA-b5611.fa --refList OceanDNA-b5611/target_genomes_gtdb.txt --output OceanDNA-b5611/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:35:40,213] [INFO] Task succeeded: fastANI
[2023-03-19 00:35:40,215] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:35:40,215] [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_002695025.1	s__Owenweeksia sp002695025	99.9561	1369	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Owenweeksia	95.0	99.94	99.87	0.98	0.96	7	conclusive
GCF_000236705.1	s__Owenweeksia hongkongensis	75.9785	71	1391	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Owenweeksia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:35:40,218] [INFO] GTDB search result was written to OceanDNA-b5611/result_gtdb.tsv
[2023-03-19 00:35:40,222] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:35:40,225] [INFO] DFAST_QC result json was written to OceanDNA-b5611/dqc_result.json
[2023-03-19 00:35:40,225] [INFO] DFAST_QC completed!
[2023-03-19 00:35:40,225] [INFO] Total running time: 0h2m21s