[2023-03-15 11:51:17,347] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:51:17,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:51:17,348] [INFO] DQC Reference Directory: /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference
[2023-03-15 11:51:18,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:51:18,950] [INFO] Task started: Prodigal
[2023-03-15 11:51:18,950] [INFO] Running command: cat /var/lib/cwl/stgc9b27140-7cd8-48d4-916d-8349ff55da41/OceanDNA-b17114.fa | prodigal -d OceanDNA-b17114/cds.fna -a OceanDNA-b17114/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:51:45,774] [INFO] Task succeeded: Prodigal
[2023-03-15 11:51:45,774] [INFO] Task started: HMMsearch
[2023-03-15 11:51:45,774] [INFO] Running command: hmmsearch --tblout OceanDNA-b17114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/reference_markers.hmm OceanDNA-b17114/protein.faa > /dev/null
[2023-03-15 11:51:46,038] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:51:46,039] [INFO] Found 6/6 markers.
[2023-03-15 11:51:46,069] [INFO] Query marker FASTA was written to OceanDNA-b17114/markers.fasta
[2023-03-15 11:51:46,070] [INFO] Task started: Blastn
[2023-03-15 11:51:46,070] [INFO] Running command: blastn -query OceanDNA-b17114/markers.fasta -db /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/reference_markers.fasta -out OceanDNA-b17114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:51:46,593] [INFO] Task succeeded: Blastn
[2023-03-15 11:51:46,594] [INFO] Selected 16 target genomes.
[2023-03-15 11:51:46,594] [INFO] Target genome list was writen to OceanDNA-b17114/target_genomes.txt
[2023-03-15 11:51:46,605] [INFO] Task started: fastANI
[2023-03-15 11:51:46,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9b27140-7cd8-48d4-916d-8349ff55da41/OceanDNA-b17114.fa --refList OceanDNA-b17114/target_genomes.txt --output OceanDNA-b17114/fastani_result.tsv --threads 1
[2023-03-15 11:51:57,891] [INFO] Task succeeded: fastANI
[2023-03-15 11:51:57,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:51:57,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:51:57,897] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:51:57,898] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:51:57,898] [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 toluolica	strain=Tol2	GCA_000307105.1	28223	28223	type	True	78.8819	436	1532	95	below_threshold
Desulfobacula phenolica	strain=DSM 3384	GCA_900105645.1	90732	90732	type	True	78.8369	434	1532	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	77.1452	119	1532	95	below_threshold
Desulfotignum balticum	strain=DSM 7044	GCA_000421285.1	115781	115781	type	True	76.9548	111	1532	95	below_threshold
Desulfotignum phosphitoxidans	strain=DSM 13687	GCA_000350545.1	190898	190898	type	True	76.8557	109	1532	95	below_threshold
Desulfobacter latus	strain=AcRS2	GCA_013389365.1	2292	2292	type	True	76.0604	72	1532	95	below_threshold
Desulfonema limicola	strain=5ac10	GCA_017377355.1	45656	45656	type	True	75.2305	52	1532	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:51:57,898] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17114/tc_result.tsv
[2023-03-15 11:51:57,898] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:51:57,898] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:51:57,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/checkm_data
[2023-03-15 11:51:57,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:51:57,905] [INFO] Task started: CheckM
[2023-03-15 11:51:57,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17114/checkm_input OceanDNA-b17114/checkm_result
[2023-03-15 11:53:03,862] [INFO] Task succeeded: CheckM
[2023-03-15 11:53:03,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.91%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:53:03,865] [INFO] ===== Completeness check finished =====
[2023-03-15 11:53:03,866] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:53:03,866] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17114/markers.fasta)
[2023-03-15 11:53:03,867] [INFO] Task started: Blastn
[2023-03-15 11:53:03,867] [INFO] Running command: blastn -query OceanDNA-b17114/markers.fasta -db /var/lib/cwl/stgf661a417-2723-4036-85ab-2d670aa090e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:53:04,600] [INFO] Task succeeded: Blastn
[2023-03-15 11:53:04,601] [INFO] Selected 9 target genomes.
[2023-03-15 11:53:04,601] [INFO] Target genome list was writen to OceanDNA-b17114/target_genomes_gtdb.txt
[2023-03-15 11:53:04,612] [INFO] Task started: fastANI
[2023-03-15 11:53:04,612] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9b27140-7cd8-48d4-916d-8349ff55da41/OceanDNA-b17114.fa --refList OceanDNA-b17114/target_genomes_gtdb.txt --output OceanDNA-b17114/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:53:12,905] [INFO] Task succeeded: fastANI
[2023-03-15 11:53:12,910] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:53:12,910] [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_018645325.1	s__Desulfobacula sp018645325	99.7386	1282	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	99.75	99.49	0.93	0.81	13	conclusive
GCA_018702715.1	s__Desulfobacula sp018702715	84.21	637	1532	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	83.9116	844	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	99.72	99.72	0.86	0.86	2	-
GCA_018812385.1	s__Desulfobacula sp018812385	83.8196	609	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237455.1	s__Desulfobacula sp014237455	80.7494	580	1532	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	80.537	428	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	98.83	98.83	0.82	0.82	2	-
GCA_003647385.1	s__Desulfobacula sp003647385	79.4792	360	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307105.1	s__Desulfobacula toluolica	78.8666	437	1532	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfobacula	95.0	97.14	97.14	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:53:12,911] [INFO] GTDB search result was written to OceanDNA-b17114/result_gtdb.tsv
[2023-03-15 11:53:12,911] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:53:12,912] [INFO] DFAST_QC result json was written to OceanDNA-b17114/dqc_result.json
[2023-03-15 11:53:12,912] [INFO] DFAST_QC completed!
[2023-03-15 11:53:12,912] [INFO] Total running time: 0h1m56s