[2023-03-18 20:40:39,435] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference
[2023-03-18 20:40:41,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,209] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stg66b62a69-690d-4b0b-99f7-61c35745c6ca/OceanDNA-b13158.fa | prodigal -d OceanDNA-b13158/cds.fna -a OceanDNA-b13158/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:53,837] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:53,837] [INFO] Task started: HMMsearch
[2023-03-18 20:40:53,837] [INFO] Running command: hmmsearch --tblout OceanDNA-b13158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/reference_markers.hmm OceanDNA-b13158/protein.faa > /dev/null
[2023-03-18 20:40:54,048] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:54,049] [INFO] Found 6/6 markers.
[2023-03-18 20:40:54,063] [INFO] Query marker FASTA was written to OceanDNA-b13158/markers.fasta
[2023-03-18 20:40:54,063] [INFO] Task started: Blastn
[2023-03-18 20:40:54,063] [INFO] Running command: blastn -query OceanDNA-b13158/markers.fasta -db /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/reference_markers.fasta -out OceanDNA-b13158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:54,626] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:54,627] [INFO] Selected 19 target genomes.
[2023-03-18 20:40:54,627] [INFO] Target genome list was writen to OceanDNA-b13158/target_genomes.txt
[2023-03-18 20:40:54,634] [INFO] Task started: fastANI
[2023-03-18 20:40:54,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b62a69-690d-4b0b-99f7-61c35745c6ca/OceanDNA-b13158.fa --refList OceanDNA-b13158/target_genomes.txt --output OceanDNA-b13158/fastani_result.tsv --threads 1
[2023-03-18 20:41:02,986] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:02,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:02,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:02,990] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:02,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:02,990] [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	76.3208	67	794	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:02,990] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13158/tc_result.tsv
[2023-03-18 20:41:02,990] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:02,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:02,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/checkm_data
[2023-03-18 20:41:02,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:03,000] [INFO] Task started: CheckM
[2023-03-18 20:41:03,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13158/checkm_input OceanDNA-b13158/checkm_result
[2023-03-18 20:41:38,111] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:38,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:38,114] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:38,114] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:38,114] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13158/markers.fasta)
[2023-03-18 20:41:38,115] [INFO] Task started: Blastn
[2023-03-18 20:41:38,115] [INFO] Running command: blastn -query OceanDNA-b13158/markers.fasta -db /var/lib/cwl/stgcacd3896-cd9e-4e54-a101-38a80c3f4454/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:38,874] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:38,875] [INFO] Selected 19 target genomes.
[2023-03-18 20:41:38,875] [INFO] Target genome list was writen to OceanDNA-b13158/target_genomes_gtdb.txt
[2023-03-18 20:41:38,980] [INFO] Task started: fastANI
[2023-03-18 20:41:38,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg66b62a69-690d-4b0b-99f7-61c35745c6ca/OceanDNA-b13158.fa --refList OceanDNA-b13158/target_genomes_gtdb.txt --output OceanDNA-b13158/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:49,127] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:49,132] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:49,132] [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_002720865.1	s__GCA-2720865 sp002720865	76.5147	51	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2720865	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210915.2	s__Halobacteriovorax marinus	76.3505	66	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	98.02	98.02	0.94	0.94	2	-
GCA_002366565.1	s__Halobacteriovorax sp002366565	76.1827	62	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002753895.1	s__Halobacteriovorax sp002753895	76.108	63	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712005.1	s__GCA-2712005 sp002712005	76.1022	54	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2712005	95.0	99.67	98.81	0.99	0.95	5	-
GCA_017858255.1	s__GCA-2712005 sp017858255	75.9233	53	794	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2712005	95.0	99.14	99.14	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:49,132] [INFO] GTDB search result was written to OceanDNA-b13158/result_gtdb.tsv
[2023-03-18 20:41:49,132] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:49,133] [INFO] DFAST_QC result json was written to OceanDNA-b13158/dqc_result.json
[2023-03-18 20:41:49,133] [INFO] DFAST_QC completed!
[2023-03-18 20:41:49,133] [INFO] Total running time: 0h1m10s