[2023-03-15 08:55:06,635] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,635] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,635] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference
[2023-03-15 08:55:08,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,347] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,347] [INFO] Running command: cat /var/lib/cwl/stg523ac4a7-4854-4412-a386-02afd37f282f/OceanDNA-b10974.fa | prodigal -d OceanDNA-b10974/cds.fna -a OceanDNA-b10974/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:16,259] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:16,259] [INFO] Task started: HMMsearch
[2023-03-15 08:55:16,259] [INFO] Running command: hmmsearch --tblout OceanDNA-b10974/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/reference_markers.hmm OceanDNA-b10974/protein.faa > /dev/null
[2023-03-15 08:55:16,507] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:16,508] [INFO] Found 6/6 markers.
[2023-03-15 08:55:16,519] [INFO] Query marker FASTA was written to OceanDNA-b10974/markers.fasta
[2023-03-15 08:55:16,520] [INFO] Task started: Blastn
[2023-03-15 08:55:16,520] [INFO] Running command: blastn -query OceanDNA-b10974/markers.fasta -db /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/reference_markers.fasta -out OceanDNA-b10974/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:17,105] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:17,105] [INFO] Selected 25 target genomes.
[2023-03-15 08:55:17,106] [INFO] Target genome list was writen to OceanDNA-b10974/target_genomes.txt
[2023-03-15 08:55:17,116] [INFO] Task started: fastANI
[2023-03-15 08:55:17,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg523ac4a7-4854-4412-a386-02afd37f282f/OceanDNA-b10974.fa --refList OceanDNA-b10974/target_genomes.txt --output OceanDNA-b10974/fastani_result.tsv --threads 1
[2023-03-15 08:55:31,213] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:31,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:31,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:31,217] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:31,217] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:31,217] [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
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	75.1185	57	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:31,217] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10974/tc_result.tsv
[2023-03-15 08:55:31,217] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:31,217] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:31,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/checkm_data
[2023-03-15 08:55:31,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:31,221] [INFO] Task started: CheckM
[2023-03-15 08:55:31,221] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10974/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10974/checkm_input OceanDNA-b10974/checkm_result
[2023-03-15 08:55:55,701] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:55,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:55,704] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:55,704] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:55,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10974/markers.fasta)
[2023-03-15 08:55:55,704] [INFO] Task started: Blastn
[2023-03-15 08:55:55,704] [INFO] Running command: blastn -query OceanDNA-b10974/markers.fasta -db /var/lib/cwl/stgdaa00f92-e2a2-4d6b-9f4e-10c19a76e33f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10974/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:56,675] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:56,676] [INFO] Selected 30 target genomes.
[2023-03-15 08:55:56,676] [INFO] Target genome list was writen to OceanDNA-b10974/target_genomes_gtdb.txt
[2023-03-15 08:55:56,768] [INFO] Task started: fastANI
[2023-03-15 08:55:56,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg523ac4a7-4854-4412-a386-02afd37f282f/OceanDNA-b10974.fa --refList OceanDNA-b10974/target_genomes_gtdb.txt --output OceanDNA-b10974/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:56:08,858] [INFO] Task succeeded: fastANI
[2023-03-15 08:56:08,864] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:56:08,864] [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_902514625.1	s__TMED220 sp902514625	77.2673	114	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905381055.1	s__TMED220 sp905381055	77.2356	163	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	76.1358	64	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_002711185.1	s__GCA-002723295 sp002711185	76.0866	60	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	98.54	98.54	0.83	0.83	2	-
GCA_002719315.1	s__GCA-2719315 sp002719315	75.9678	90	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182305.1	s__MS024-2A sp905182305	75.7634	53	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480425.1	s__MS024-2A sp905480425	75.7291	53	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MS024-2A	95.0	95.11	95.11	0.87	0.87	2	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	75.6571	52	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260195.1	s__Lutibacter citreus	75.1185	57	446	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:56:08,864] [INFO] GTDB search result was written to OceanDNA-b10974/result_gtdb.tsv
[2023-03-15 08:56:08,864] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:56:08,865] [INFO] DFAST_QC result json was written to OceanDNA-b10974/dqc_result.json
[2023-03-15 08:56:08,865] [INFO] DFAST_QC completed!
[2023-03-15 08:56:08,865] [INFO] Total running time: 0h1m2s