[2023-03-17 08:39:27,325] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:39:27,325] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:39:27,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference
[2023-03-17 08:39:28,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:39:28,534] [INFO] Task started: Prodigal
[2023-03-17 08:39:28,534] [INFO] Running command: cat /var/lib/cwl/stga3f113dd-79d7-434c-a5ee-7aa13cb5f5db/OceanDNA-b22478.fa | prodigal -d OceanDNA-b22478/cds.fna -a OceanDNA-b22478/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:39:45,730] [INFO] Task succeeded: Prodigal
[2023-03-17 08:39:45,730] [INFO] Task started: HMMsearch
[2023-03-17 08:39:45,731] [INFO] Running command: hmmsearch --tblout OceanDNA-b22478/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/reference_markers.hmm OceanDNA-b22478/protein.faa > /dev/null
[2023-03-17 08:39:45,955] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:39:45,955] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga3f113dd-79d7-434c-a5ee-7aa13cb5f5db/OceanDNA-b22478.fa]
[2023-03-17 08:39:45,989] [INFO] Query marker FASTA was written to OceanDNA-b22478/markers.fasta
[2023-03-17 08:39:45,990] [INFO] Task started: Blastn
[2023-03-17 08:39:45,990] [INFO] Running command: blastn -query OceanDNA-b22478/markers.fasta -db /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/reference_markers.fasta -out OceanDNA-b22478/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:39:46,530] [INFO] Task succeeded: Blastn
[2023-03-17 08:39:46,531] [INFO] Selected 28 target genomes.
[2023-03-17 08:39:46,531] [INFO] Target genome list was writen to OceanDNA-b22478/target_genomes.txt
[2023-03-17 08:39:46,731] [INFO] Task started: fastANI
[2023-03-17 08:39:46,732] [INFO] Running command: fastANI --query /var/lib/cwl/stga3f113dd-79d7-434c-a5ee-7aa13cb5f5db/OceanDNA-b22478.fa --refList OceanDNA-b22478/target_genomes.txt --output OceanDNA-b22478/fastani_result.tsv --threads 1
[2023-03-17 08:40:14,102] [INFO] Task succeeded: fastANI
[2023-03-17 08:40:14,102] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:40:14,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:40:14,106] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:40:14,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:40:14,106] [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
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.6665	59	604	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.5636	56	604	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:40:14,106] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22478/tc_result.tsv
[2023-03-17 08:40:14,106] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:40:14,106] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:40:14,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/checkm_data
[2023-03-17 08:40:14,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:40:14,113] [INFO] Task started: CheckM
[2023-03-17 08:40:14,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22478/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22478/checkm_input OceanDNA-b22478/checkm_result
[2023-03-17 08:41:01,318] [INFO] Task succeeded: CheckM
[2023-03-17 08:41:01,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.41%
Contamintation: 0.98%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:41:01,322] [INFO] ===== Completeness check finished =====
[2023-03-17 08:41:01,322] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:41:01,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22478/markers.fasta)
[2023-03-17 08:41:01,323] [INFO] Task started: Blastn
[2023-03-17 08:41:01,323] [INFO] Running command: blastn -query OceanDNA-b22478/markers.fasta -db /var/lib/cwl/stgc8532afa-41e9-49fd-b8d8-6a9becb5a59e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22478/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:41:02,098] [INFO] Task succeeded: Blastn
[2023-03-17 08:41:02,739] [INFO] Selected 21 target genomes.
[2023-03-17 08:41:02,739] [INFO] Target genome list was writen to OceanDNA-b22478/target_genomes_gtdb.txt
[2023-03-17 08:41:03,446] [INFO] Task started: fastANI
[2023-03-17 08:41:03,446] [INFO] Running command: fastANI --query /var/lib/cwl/stga3f113dd-79d7-434c-a5ee-7aa13cb5f5db/OceanDNA-b22478.fa --refList OceanDNA-b22478/target_genomes_gtdb.txt --output OceanDNA-b22478/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:41:27,035] [INFO] Task succeeded: fastANI
[2023-03-17 08:41:27,038] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:41:27,039] [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_007745635.1	s__Stieleria sp002167455	81.9362	481	604	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	98.72	98.72	0.91	0.91	2	-
GCF_008035925.1	s__Stieleria maiorica	76.6665	59	604	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	76.5636	56	604	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.3807	55	604	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.2972	60	604	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:41:27,039] [INFO] GTDB search result was written to OceanDNA-b22478/result_gtdb.tsv
[2023-03-17 08:41:27,039] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:41:27,040] [INFO] DFAST_QC result json was written to OceanDNA-b22478/dqc_result.json
[2023-03-17 08:41:27,040] [INFO] DFAST_QC completed!
[2023-03-17 08:41:27,040] [INFO] Total running time: 0h1m60s