[2023-03-18 03:45:10,235] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,235] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,235] [INFO] DQC Reference Directory: /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference
[2023-03-18 03:45:11,967] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:11,968] [INFO] Task started: Prodigal
[2023-03-18 03:45:11,968] [INFO] Running command: cat /var/lib/cwl/stg254f320a-7710-41db-a272-54c86ec234bb/OceanDNA-b17697.fa | prodigal -d OceanDNA-b17697/cds.fna -a OceanDNA-b17697/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:41,439] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:41,439] [INFO] Task started: HMMsearch
[2023-03-18 03:45:41,439] [INFO] Running command: hmmsearch --tblout OceanDNA-b17697/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/reference_markers.hmm OceanDNA-b17697/protein.faa > /dev/null
[2023-03-18 03:45:41,688] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:41,689] [INFO] Found 6/6 markers.
[2023-03-18 03:45:41,724] [INFO] Query marker FASTA was written to OceanDNA-b17697/markers.fasta
[2023-03-18 03:45:41,725] [INFO] Task started: Blastn
[2023-03-18 03:45:41,725] [INFO] Running command: blastn -query OceanDNA-b17697/markers.fasta -db /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/reference_markers.fasta -out OceanDNA-b17697/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:42,274] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:42,275] [INFO] Selected 28 target genomes.
[2023-03-18 03:45:42,275] [INFO] Target genome list was writen to OceanDNA-b17697/target_genomes.txt
[2023-03-18 03:45:42,288] [INFO] Task started: fastANI
[2023-03-18 03:45:42,288] [INFO] Running command: fastANI --query /var/lib/cwl/stg254f320a-7710-41db-a272-54c86ec234bb/OceanDNA-b17697.fa --refList OceanDNA-b17697/target_genomes.txt --output OceanDNA-b17697/fastani_result.tsv --threads 1
[2023-03-18 03:46:02,713] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:02,713] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:46:02,713] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:46:02,719] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:46:02,719] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:46:02,719] [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
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	74.8796	86	1593	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	74.879	86	1593	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	74.8615	68	1593	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	74.815	57	1593	95	below_threshold
Tsukamurella conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	74.6385	58	1593	95	below_threshold
Persicimonas caeni	strain=YN101	GCA_006517175.1	2292766	2292766	type	True	74.6373	54	1593	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	74.5921	88	1593	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:46:02,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17697/tc_result.tsv
[2023-03-18 03:46:02,719] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:46:02,719] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:46:02,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/checkm_data
[2023-03-18 03:46:02,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:46:02,727] [INFO] Task started: CheckM
[2023-03-18 03:46:02,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17697/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17697/checkm_input OceanDNA-b17697/checkm_result
[2023-03-18 03:47:12,344] [INFO] Task succeeded: CheckM
[2023-03-18 03:47:12,345] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.85%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:47:12,348] [INFO] ===== Completeness check finished =====
[2023-03-18 03:47:12,348] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:47:12,348] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17697/markers.fasta)
[2023-03-18 03:47:12,349] [INFO] Task started: Blastn
[2023-03-18 03:47:12,349] [INFO] Running command: blastn -query OceanDNA-b17697/markers.fasta -db /var/lib/cwl/stgf375d4b6-f42f-4989-89a9-255a5631b158/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17697/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:47:13,162] [INFO] Task succeeded: Blastn
[2023-03-18 03:47:13,163] [INFO] Selected 18 target genomes.
[2023-03-18 03:47:13,163] [INFO] Target genome list was writen to OceanDNA-b17697/target_genomes_gtdb.txt
[2023-03-18 03:47:13,447] [INFO] Task started: fastANI
[2023-03-18 03:47:13,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg254f320a-7710-41db-a272-54c86ec234bb/OceanDNA-b17697.fa --refList OceanDNA-b17697/target_genomes_gtdb.txt --output OceanDNA-b17697/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:47:26,568] [INFO] Task succeeded: fastANI
[2023-03-18 03:47:26,574] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:47:26,574] [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_002724215.1	s__GCA-2724215 sp002724215	99.2646	1443	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018672475.1	s__GCA-2724215 sp018672475	77.9829	702	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	-
GCA_015660315.1	s__GCA-2724215 sp015660315	77.9492	547	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840005.1	s__GCA-2724215 sp009840005	77.3499	443	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009841115.1	s__GCA-2724215 sp009841115	77.3231	422	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009845645.1	s__GCA-2724215 sp009845645	77.1731	278	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	77.1437	366	1593	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	74.815	57	1593	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002420005.1	s__UBA5704 sp002420005	74.73	62	1593	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:47:26,574] [INFO] GTDB search result was written to OceanDNA-b17697/result_gtdb.tsv
[2023-03-18 03:47:26,574] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:47:26,575] [INFO] DFAST_QC result json was written to OceanDNA-b17697/dqc_result.json
[2023-03-18 03:47:26,575] [INFO] DFAST_QC completed!
[2023-03-18 03:47:26,575] [INFO] Total running time: 0h2m16s