[2023-03-15 05:29:12,508] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:12,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:12,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference
[2023-03-15 05:29:13,683] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:13,683] [INFO] Task started: Prodigal
[2023-03-15 05:29:13,683] [INFO] Running command: cat /var/lib/cwl/stg11320069-df84-462d-bd13-abf3bff6ca93/OceanDNA-b13159.fa | prodigal -d OceanDNA-b13159/cds.fna -a OceanDNA-b13159/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:29,073] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:29,073] [INFO] Task started: HMMsearch
[2023-03-15 05:29:29,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b13159/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/reference_markers.hmm OceanDNA-b13159/protein.faa > /dev/null
[2023-03-15 05:29:29,359] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:29,360] [INFO] Found 6/6 markers.
[2023-03-15 05:29:29,381] [INFO] Query marker FASTA was written to OceanDNA-b13159/markers.fasta
[2023-03-15 05:29:29,382] [INFO] Task started: Blastn
[2023-03-15 05:29:29,382] [INFO] Running command: blastn -query OceanDNA-b13159/markers.fasta -db /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/reference_markers.fasta -out OceanDNA-b13159/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:29,970] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:29,971] [INFO] Selected 25 target genomes.
[2023-03-15 05:29:29,971] [INFO] Target genome list was writen to OceanDNA-b13159/target_genomes.txt
[2023-03-15 05:29:29,983] [INFO] Task started: fastANI
[2023-03-15 05:29:29,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg11320069-df84-462d-bd13-abf3bff6ca93/OceanDNA-b13159.fa --refList OceanDNA-b13159/target_genomes.txt --output OceanDNA-b13159/fastani_result.tsv --threads 1
[2023-03-15 05:29:42,704] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:42,704] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:42,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:42,708] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:42,709] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:29:42,709] [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
Halobacteriovorax marinus	strain=SJ	GCA_000210915.2	97084	97084	type	True	76.3296	56	973	95	below_threshold
Halobacteriovorax vibrionivorans	strain=BL9	GCA_003346865.1	2152716	2152716	type	True	75.9731	52	973	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:29:42,709] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13159/tc_result.tsv
[2023-03-15 05:29:42,709] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:42,709] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:42,709] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/checkm_data
[2023-03-15 05:29:42,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:42,715] [INFO] Task started: CheckM
[2023-03-15 05:29:42,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13159/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13159/checkm_input OceanDNA-b13159/checkm_result
[2023-03-15 05:30:24,074] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:24,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:24,077] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:24,077] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:24,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13159/markers.fasta)
[2023-03-15 05:30:24,078] [INFO] Task started: Blastn
[2023-03-15 05:30:24,078] [INFO] Running command: blastn -query OceanDNA-b13159/markers.fasta -db /var/lib/cwl/stg1c0d6e91-08b5-466d-90f7-73e1dfbda72f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13159/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:24,830] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:24,831] [INFO] Selected 22 target genomes.
[2023-03-15 05:30:24,831] [INFO] Target genome list was writen to OceanDNA-b13159/target_genomes_gtdb.txt
[2023-03-15 05:30:24,848] [INFO] Task started: fastANI
[2023-03-15 05:30:24,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg11320069-df84-462d-bd13-abf3bff6ca93/OceanDNA-b13159.fa --refList OceanDNA-b13159/target_genomes_gtdb.txt --output OceanDNA-b13159/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:36,778] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:36,783] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:30:36,783] [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_002712005.1	s__GCA-2712005 sp002712005	98.8287	960	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2712005	95.0	99.67	98.81	0.99	0.95	5	conclusive
GCA_017858255.1	s__GCA-2712005 sp017858255	76.6231	82	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2712005	95.0	99.14	99.14	0.90	0.90	2	-
GCA_002753895.1	s__Halobacteriovorax sp002753895	76.4615	51	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210915.2	s__Halobacteriovorax marinus	76.3996	53	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	98.02	98.02	0.94	0.94	2	-
GCF_000447755.1	s__BSW11-IV sp000447755	76.1079	52	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__BSW11-IV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447795.1	s__DB6-IX sp000447795	76.0007	51	973	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:36,783] [INFO] GTDB search result was written to OceanDNA-b13159/result_gtdb.tsv
[2023-03-15 05:30:36,784] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:36,784] [INFO] DFAST_QC result json was written to OceanDNA-b13159/dqc_result.json
[2023-03-15 05:30:36,784] [INFO] DFAST_QC completed!
[2023-03-15 05:30:36,785] [INFO] Total running time: 0h1m24s