[2023-03-15 03:14:16,427] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,427] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference
[2023-03-15 03:14:17,622] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,623] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,623] [INFO] Running command: cat /var/lib/cwl/stg61caa280-adcb-4bae-9db2-fb50ce2414fb/OceanDNA-b13140.fa | prodigal -d OceanDNA-b13140/cds.fna -a OceanDNA-b13140/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:33,215] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:33,216] [INFO] Task started: HMMsearch
[2023-03-15 03:14:33,216] [INFO] Running command: hmmsearch --tblout OceanDNA-b13140/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/reference_markers.hmm OceanDNA-b13140/protein.faa > /dev/null
[2023-03-15 03:14:33,499] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:33,500] [INFO] Found 6/6 markers.
[2023-03-15 03:14:33,523] [INFO] Query marker FASTA was written to OceanDNA-b13140/markers.fasta
[2023-03-15 03:14:33,524] [INFO] Task started: Blastn
[2023-03-15 03:14:33,524] [INFO] Running command: blastn -query OceanDNA-b13140/markers.fasta -db /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/reference_markers.fasta -out OceanDNA-b13140/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:34,053] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:34,053] [INFO] Selected 14 target genomes.
[2023-03-15 03:14:34,054] [INFO] Target genome list was writen to OceanDNA-b13140/target_genomes.txt
[2023-03-15 03:14:34,066] [INFO] Task started: fastANI
[2023-03-15 03:14:34,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg61caa280-adcb-4bae-9db2-fb50ce2414fb/OceanDNA-b13140.fa --refList OceanDNA-b13140/target_genomes.txt --output OceanDNA-b13140/fastani_result.tsv --threads 1
[2023-03-15 03:14:41,112] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:41,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:41,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:41,117] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:41,117] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:41,117] [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 vibrionivorans	strain=BL9	GCA_003346865.1	2152716	2152716	type	True	77.747	136	1003	95	below_threshold
Halobacteriovorax marinus	strain=SJ	GCA_000210915.2	97084	97084	type	True	76.6457	99	1003	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:41,117] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13140/tc_result.tsv
[2023-03-15 03:14:41,117] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:41,117] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:41,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/checkm_data
[2023-03-15 03:14:41,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:41,124] [INFO] Task started: CheckM
[2023-03-15 03:14:41,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13140/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13140/checkm_input OceanDNA-b13140/checkm_result
[2023-03-15 03:15:22,773] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:22,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:22,776] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:22,776] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:22,776] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13140/markers.fasta)
[2023-03-15 03:15:22,776] [INFO] Task started: Blastn
[2023-03-15 03:15:22,776] [INFO] Running command: blastn -query OceanDNA-b13140/markers.fasta -db /var/lib/cwl/stg20e3221d-8505-41d0-8a5f-41201fa11c59/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13140/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:23,528] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:23,529] [INFO] Selected 15 target genomes.
[2023-03-15 03:15:23,529] [INFO] Target genome list was writen to OceanDNA-b13140/target_genomes_gtdb.txt
[2023-03-15 03:15:23,539] [INFO] Task started: fastANI
[2023-03-15 03:15:23,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg61caa280-adcb-4bae-9db2-fb50ce2414fb/OceanDNA-b13140.fa --refList OceanDNA-b13140/target_genomes_gtdb.txt --output OceanDNA-b13140/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:31,598] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:31,605] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 03:15:31,605] [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_001874305.1	s__DB6-IX sp001874305	99.5363	994	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000447775.1	s__DB6-IX sp000447775	78.7689	270	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612895.1	s__DB6-IX sp003612895	77.6679	144	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	98.61	98.58	0.96	0.96	3	-
GCF_002903145.1	s__DB6-IX sp002903145	77.2891	146	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000443995.1	s__DB6-IX sp000443995	77.2885	129	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447795.1	s__DB6-IX sp000447795	77.0817	172	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366565.1	s__Halobacteriovorax sp002366565	76.969	116	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447755.1	s__BSW11-IV sp000447755	76.7719	94	1003	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_000210915.2	s__Halobacteriovorax marinus	76.6643	98	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	98.02	98.02	0.94	0.94	2	-
GCA_002163155.1	s__Halobacteriovorax marinus_A	76.516	102	1003	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:31,605] [INFO] GTDB search result was written to OceanDNA-b13140/result_gtdb.tsv
[2023-03-15 03:15:31,605] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:31,606] [INFO] DFAST_QC result json was written to OceanDNA-b13140/dqc_result.json
[2023-03-15 03:15:31,606] [INFO] DFAST_QC completed!
[2023-03-15 03:15:31,606] [INFO] Total running time: 0h1m15s