[2023-03-16 07:22:13,479] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:22:13,479] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:22:13,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference
[2023-03-16 07:22:14,572] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:22:14,573] [INFO] Task started: Prodigal
[2023-03-16 07:22:14,574] [INFO] Running command: cat /var/lib/cwl/stgedd97f08-cbc1-4c49-8d51-84da074bf206/OceanDNA-b22497.fa | prodigal -d OceanDNA-b22497/cds.fna -a OceanDNA-b22497/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:22:40,249] [INFO] Task succeeded: Prodigal
[2023-03-16 07:22:40,249] [INFO] Task started: HMMsearch
[2023-03-16 07:22:40,249] [INFO] Running command: hmmsearch --tblout OceanDNA-b22497/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/reference_markers.hmm OceanDNA-b22497/protein.faa > /dev/null
[2023-03-16 07:22:40,515] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:22:40,516] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgedd97f08-cbc1-4c49-8d51-84da074bf206/OceanDNA-b22497.fa]
[2023-03-16 07:22:40,545] [INFO] Query marker FASTA was written to OceanDNA-b22497/markers.fasta
[2023-03-16 07:22:40,547] [INFO] Task started: Blastn
[2023-03-16 07:22:40,547] [INFO] Running command: blastn -query OceanDNA-b22497/markers.fasta -db /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/reference_markers.fasta -out OceanDNA-b22497/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:22:41,379] [INFO] Task succeeded: Blastn
[2023-03-16 07:22:41,380] [INFO] Selected 21 target genomes.
[2023-03-16 07:22:41,380] [INFO] Target genome list was writen to OceanDNA-b22497/target_genomes.txt
[2023-03-16 07:22:41,442] [INFO] Task started: fastANI
[2023-03-16 07:22:41,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd97f08-cbc1-4c49-8d51-84da074bf206/OceanDNA-b22497.fa --refList OceanDNA-b22497/target_genomes.txt --output OceanDNA-b22497/fastani_result.tsv --threads 1
[2023-03-16 07:23:03,383] [INFO] Task succeeded: fastANI
[2023-03-16 07:23:03,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:23:03,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:23:03,520] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:23:03,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:23:03,520] [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
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	75.8683	52	1364	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:23:03,520] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22497/tc_result.tsv
[2023-03-16 07:23:03,521] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:23:03,521] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:23:03,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/checkm_data
[2023-03-16 07:23:03,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:23:03,528] [INFO] Task started: CheckM
[2023-03-16 07:23:03,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22497/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22497/checkm_input OceanDNA-b22497/checkm_result
[2023-03-16 07:24:11,335] [INFO] Task succeeded: CheckM
[2023-03-16 07:24:11,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 07:24:11,343] [INFO] ===== Completeness check finished =====
[2023-03-16 07:24:11,343] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:24:11,343] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22497/markers.fasta)
[2023-03-16 07:24:11,345] [INFO] Task started: Blastn
[2023-03-16 07:24:11,345] [INFO] Running command: blastn -query OceanDNA-b22497/markers.fasta -db /var/lib/cwl/stg9ba74985-a7b3-4e06-a770-45e4c1750d0d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22497/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:24:12,534] [INFO] Task succeeded: Blastn
[2023-03-16 07:24:12,535] [INFO] Selected 10 target genomes.
[2023-03-16 07:24:12,535] [INFO] Target genome list was writen to OceanDNA-b22497/target_genomes_gtdb.txt
[2023-03-16 07:24:12,680] [INFO] Task started: fastANI
[2023-03-16 07:24:12,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgedd97f08-cbc1-4c49-8d51-84da074bf206/OceanDNA-b22497.fa --refList OceanDNA-b22497/target_genomes_gtdb.txt --output OceanDNA-b22497/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:24:24,971] [INFO] Task succeeded: fastANI
[2023-03-16 07:24:24,975] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:24:24,975] [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_002712845.1	s__Rubripirellula sp002712845	99.0842	529	1364	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003513555.1	s__Rubripirellula sp003513555	86.2202	1073	1364	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689655.1	s__Rubripirellula sp002689655	84.2922	1063	1364	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	100.00	100.00	0.98	0.98	2	-
GCA_002690925.1	s__Rubripirellula sp002690925	84.0666	978	1364	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	80.7311	744	1364	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:24:24,976] [INFO] GTDB search result was written to OceanDNA-b22497/result_gtdb.tsv
[2023-03-16 07:24:24,976] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:24:24,976] [INFO] DFAST_QC result json was written to OceanDNA-b22497/dqc_result.json
[2023-03-16 07:24:24,976] [INFO] DFAST_QC completed!
[2023-03-16 07:24:24,977] [INFO] Total running time: 0h2m11s