[2023-03-19 00:33:19,066] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:33:19,066] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:33:19,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference
[2023-03-19 00:33:20,258] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:33:20,258] [INFO] Task started: Prodigal
[2023-03-19 00:33:20,258] [INFO] Running command: cat /var/lib/cwl/stg01c4d60e-3a20-4f56-a30d-8978a15aba1c/OceanDNA-b17091.fa | prodigal -d OceanDNA-b17091/cds.fna -a OceanDNA-b17091/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:33:37,659] [INFO] Task succeeded: Prodigal
[2023-03-19 00:33:37,660] [INFO] Task started: HMMsearch
[2023-03-19 00:33:37,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b17091/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/reference_markers.hmm OceanDNA-b17091/protein.faa > /dev/null
[2023-03-19 00:33:37,968] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:33:37,969] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg01c4d60e-3a20-4f56-a30d-8978a15aba1c/OceanDNA-b17091.fa]
[2023-03-19 00:33:38,002] [INFO] Query marker FASTA was written to OceanDNA-b17091/markers.fasta
[2023-03-19 00:33:38,004] [INFO] Task started: Blastn
[2023-03-19 00:33:38,004] [INFO] Running command: blastn -query OceanDNA-b17091/markers.fasta -db /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/reference_markers.fasta -out OceanDNA-b17091/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:33:38,603] [INFO] Task succeeded: Blastn
[2023-03-19 00:33:38,608] [INFO] Selected 14 target genomes.
[2023-03-19 00:33:38,608] [INFO] Target genome list was writen to OceanDNA-b17091/target_genomes.txt
[2023-03-19 00:33:38,619] [INFO] Task started: fastANI
[2023-03-19 00:33:38,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c4d60e-3a20-4f56-a30d-8978a15aba1c/OceanDNA-b17091.fa --refList OceanDNA-b17091/target_genomes.txt --output OceanDNA-b17091/fastani_result.tsv --threads 1
[2023-03-19 00:33:48,061] [INFO] Task succeeded: fastANI
[2023-03-19 00:33:48,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:33:48,062] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:33:48,069] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:33:48,069] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:33:48,069] [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
Desulfobacula phenolica	strain=DSM 3384	GCA_900105645.1	90732	90732	type	True	79.8391	427	998	95	below_threshold
Desulfobacula toluolica	strain=Tol2	GCA_000307105.1	28223	28223	type	True	79.656	437	998	95	below_threshold
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	76.7999	90	998	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	76.5739	116	998	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	76.3754	94	998	95	below_threshold
Desulfobacter hydrogenophilus	strain=DSM 3380	GCA_010499545.1	2291	2291	type	True	76.3648	61	998	95	below_threshold
Desulfobacter vibrioformis	strain=DSM 8776	GCA_000745975.1	34031	34031	type	True	76.2766	71	998	95	below_threshold
Desulfobacter curvatus	strain=DSM 3379	GCA_000373985.1	2290	2290	type	True	76.1494	58	998	95	below_threshold
Desulfocicer vacuolatum	strain=DSM 3385	GCA_900176365.1	2298	2298	type	True	76.1	70	998	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:33:48,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17091/tc_result.tsv
[2023-03-19 00:33:48,076] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:33:48,076] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:33:48,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/checkm_data
[2023-03-19 00:33:48,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:33:48,085] [INFO] Task started: CheckM
[2023-03-19 00:33:48,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17091/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17091/checkm_input OceanDNA-b17091/checkm_result
[2023-03-19 00:34:33,845] [INFO] Task succeeded: CheckM
[2023-03-19 00:34:33,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:34:33,850] [INFO] ===== Completeness check finished =====
[2023-03-19 00:34:33,850] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:34:33,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17091/markers.fasta)
[2023-03-19 00:34:33,851] [INFO] Task started: Blastn
[2023-03-19 00:34:33,851] [INFO] Running command: blastn -query OceanDNA-b17091/markers.fasta -db /var/lib/cwl/stg01bf7e62-4623-4180-9176-a3bcbadacf0f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17091/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:34:34,584] [INFO] Task succeeded: Blastn
[2023-03-19 00:34:34,587] [INFO] Selected 7 target genomes.
[2023-03-19 00:34:34,587] [INFO] Target genome list was writen to OceanDNA-b17091/target_genomes_gtdb.txt
[2023-03-19 00:34:34,615] [INFO] Task started: fastANI
[2023-03-19 00:34:34,615] [INFO] Running command: fastANI --query /var/lib/cwl/stg01c4d60e-3a20-4f56-a30d-8978a15aba1c/OceanDNA-b17091.fa --refList OceanDNA-b17091/target_genomes_gtdb.txt --output OceanDNA-b17091/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:34:40,359] [INFO] Task succeeded: fastANI
[2023-03-19 00:34:40,364] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:34:40,364] [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_018812385.1	s__Desulfobacula sp018812385	91.854	571	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014383445.1	s__Desulfobacula maris	91.5685	692	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	99.72	99.72	0.86	0.86	2	-
GCA_018702715.1	s__Desulfobacula sp018702715	84.0661	486	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645325.1	s__Desulfobacula sp018645325	83.8832	640	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	99.75	99.49	0.93	0.81	13	-
GCA_014237455.1	s__Desulfobacula sp014237455	82.5698	559	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019038815.1	s__Desulfobacula sp019038815	82.2943	411	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	98.83	98.83	0.82	0.82	2	-
GCF_000307105.1	s__Desulfobacula toluolica	79.6504	438	998	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	97.14	97.14	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:34:40,366] [INFO] GTDB search result was written to OceanDNA-b17091/result_gtdb.tsv
[2023-03-19 00:34:40,367] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:34:40,370] [INFO] DFAST_QC result json was written to OceanDNA-b17091/dqc_result.json
[2023-03-19 00:34:40,370] [INFO] DFAST_QC completed!
[2023-03-19 00:34:40,370] [INFO] Total running time: 0h1m21s