[2023-03-16 07:34:40,569] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:34:40,570] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:34:40,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference
[2023-03-16 07:34:42,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:34:42,230] [INFO] Task started: Prodigal
[2023-03-16 07:34:42,230] [INFO] Running command: cat /var/lib/cwl/stg821b1609-6c21-4ae5-b51e-1863a76ca96e/OceanDNA-b5274.fa | prodigal -d OceanDNA-b5274/cds.fna -a OceanDNA-b5274/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:34:59,586] [INFO] Task succeeded: Prodigal
[2023-03-16 07:34:59,587] [INFO] Task started: HMMsearch
[2023-03-16 07:34:59,587] [INFO] Running command: hmmsearch --tblout OceanDNA-b5274/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/reference_markers.hmm OceanDNA-b5274/protein.faa > /dev/null
[2023-03-16 07:34:59,783] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:34:59,783] [INFO] Found 6/6 markers.
[2023-03-16 07:34:59,839] [INFO] Query marker FASTA was written to OceanDNA-b5274/markers.fasta
[2023-03-16 07:34:59,841] [INFO] Task started: Blastn
[2023-03-16 07:34:59,841] [INFO] Running command: blastn -query OceanDNA-b5274/markers.fasta -db /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/reference_markers.fasta -out OceanDNA-b5274/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:35:00,381] [INFO] Task succeeded: Blastn
[2023-03-16 07:35:00,382] [INFO] Selected 24 target genomes.
[2023-03-16 07:35:00,382] [INFO] Target genome list was writen to OceanDNA-b5274/target_genomes.txt
[2023-03-16 07:35:00,541] [INFO] Task started: fastANI
[2023-03-16 07:35:00,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg821b1609-6c21-4ae5-b51e-1863a76ca96e/OceanDNA-b5274.fa --refList OceanDNA-b5274/target_genomes.txt --output OceanDNA-b5274/fastani_result.tsv --threads 1
[2023-03-16 07:35:13,352] [INFO] Task succeeded: fastANI
[2023-03-16 07:35:13,353] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:35:13,353] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:35:13,358] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:35:13,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:35:13,358] [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
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	76.8214	85	828	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	76.527	89	828	95	below_threshold
Brumimicrobium aurantiacum	strain=N62	GCA_003402975.1	1737063	1737063	type	True	76.4188	89	828	95	below_threshold
Brumimicrobium salinarum	strain=LHR20	GCA_002844555.1	2058658	2058658	type	True	76.2512	76	828	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:35:13,358] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5274/tc_result.tsv
[2023-03-16 07:35:13,358] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:35:13,359] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:35:13,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/checkm_data
[2023-03-16 07:35:13,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:35:13,364] [INFO] Task started: CheckM
[2023-03-16 07:35:13,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5274/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5274/checkm_input OceanDNA-b5274/checkm_result
[2023-03-16 07:35:59,756] [INFO] Task succeeded: CheckM
[2023-03-16 07:35:59,757] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:35:59,770] [INFO] ===== Completeness check finished =====
[2023-03-16 07:35:59,770] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:35:59,770] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5274/markers.fasta)
[2023-03-16 07:35:59,771] [INFO] Task started: Blastn
[2023-03-16 07:35:59,771] [INFO] Running command: blastn -query OceanDNA-b5274/markers.fasta -db /var/lib/cwl/stg916f6d0c-3578-4c2d-888e-7ebe74ca4329/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5274/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:36:00,506] [INFO] Task succeeded: Blastn
[2023-03-16 07:36:00,507] [INFO] Selected 23 target genomes.
[2023-03-16 07:36:00,507] [INFO] Target genome list was writen to OceanDNA-b5274/target_genomes_gtdb.txt
[2023-03-16 07:36:01,302] [INFO] Task started: fastANI
[2023-03-16 07:36:01,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg821b1609-6c21-4ae5-b51e-1863a76ca96e/OceanDNA-b5274.fa --refList OceanDNA-b5274/target_genomes_gtdb.txt --output OceanDNA-b5274/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:36:13,501] [INFO] Task succeeded: fastANI
[2023-03-16 07:36:13,506] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:36:13,506] [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_002734085.1	s__Brumimicrobium sp002734085	89.6674	697	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331485.1	s__Brumimicrobium sp002331485	77.4982	92	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	76.8736	83	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143775.1	s__Brumimicrobium sp003143775	76.5882	86	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025005.1	s__Brumimicrobium mesophilum	76.527	89	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402975.1	s__Brumimicrobium aurantiacum	76.4188	89	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844555.1	s__Brumimicrobium salinarum	76.2512	76	828	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:36:13,506] [INFO] GTDB search result was written to OceanDNA-b5274/result_gtdb.tsv
[2023-03-16 07:36:13,506] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:36:13,507] [INFO] DFAST_QC result json was written to OceanDNA-b5274/dqc_result.json
[2023-03-16 07:36:13,507] [INFO] DFAST_QC completed!
[2023-03-16 07:36:13,507] [INFO] Total running time: 0h1m33s