[2023-03-15 18:25:07,900] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:25:07,900] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:25:07,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference
[2023-03-15 18:25:11,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:25:11,457] [INFO] Task started: Prodigal
[2023-03-15 18:25:11,457] [INFO] Running command: cat /var/lib/cwl/stg46eaa1af-e381-463a-a3f5-c7adfca7e70e/OceanDNA-b42.fa | prodigal -d OceanDNA-b42/cds.fna -a OceanDNA-b42/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:25:39,093] [INFO] Task succeeded: Prodigal
[2023-03-15 18:25:39,093] [INFO] Task started: HMMsearch
[2023-03-15 18:25:39,093] [INFO] Running command: hmmsearch --tblout OceanDNA-b42/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/reference_markers.hmm OceanDNA-b42/protein.faa > /dev/null
[2023-03-15 18:25:39,338] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:25:39,339] [INFO] Found 6/6 markers.
[2023-03-15 18:25:39,381] [INFO] Query marker FASTA was written to OceanDNA-b42/markers.fasta
[2023-03-15 18:25:39,382] [INFO] Task started: Blastn
[2023-03-15 18:25:39,382] [INFO] Running command: blastn -query OceanDNA-b42/markers.fasta -db /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/reference_markers.fasta -out OceanDNA-b42/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:25:40,003] [INFO] Task succeeded: Blastn
[2023-03-15 18:25:40,004] [INFO] Selected 22 target genomes.
[2023-03-15 18:25:40,004] [INFO] Target genome list was writen to OceanDNA-b42/target_genomes.txt
[2023-03-15 18:25:40,018] [INFO] Task started: fastANI
[2023-03-15 18:25:40,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg46eaa1af-e381-463a-a3f5-c7adfca7e70e/OceanDNA-b42.fa --refList OceanDNA-b42/target_genomes.txt --output OceanDNA-b42/fastani_result.tsv --threads 1
[2023-03-15 18:26:03,087] [INFO] Task succeeded: fastANI
[2023-03-15 18:26:03,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:26:03,088] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:26:03,093] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:26:03,093] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:26:03,093] [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
Streptomyces orinoci	strain=NRRL B-3379	GCA_003121295.1	67339	67339	type	True	74.7665	60	1315	95	below_threshold
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	74.6949	73	1315	95	below_threshold
Actinoplanes abujensis	strain=DSM 45518	GCA_014204895.1	882441	882441	type	True	74.686	99	1315	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	74.6782	86	1315	95	below_threshold
Streptomyces violaceochromogenes	strain=JCM 4530	GCA_014650235.1	67377	67377	type	True	74.6706	77	1315	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:26:03,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42/tc_result.tsv
[2023-03-15 18:26:03,093] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:26:03,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:26:03,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/checkm_data
[2023-03-15 18:26:03,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:26:03,102] [INFO] Task started: CheckM
[2023-03-15 18:26:03,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42/checkm_input OceanDNA-b42/checkm_result
[2023-03-15 18:27:10,335] [INFO] Task succeeded: CheckM
[2023-03-15 18:27:10,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:27:10,339] [INFO] ===== Completeness check finished =====
[2023-03-15 18:27:10,339] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:27:10,339] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42/markers.fasta)
[2023-03-15 18:27:10,341] [INFO] Task started: Blastn
[2023-03-15 18:27:10,341] [INFO] Running command: blastn -query OceanDNA-b42/markers.fasta -db /var/lib/cwl/stg16830d17-8a42-4d7a-9876-2b65102154b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:27:11,484] [INFO] Task succeeded: Blastn
[2023-03-15 18:27:11,485] [INFO] Selected 25 target genomes.
[2023-03-15 18:27:11,485] [INFO] Target genome list was writen to OceanDNA-b42/target_genomes_gtdb.txt
[2023-03-15 18:27:12,812] [INFO] Task started: fastANI
[2023-03-15 18:27:12,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg46eaa1af-e381-463a-a3f5-c7adfca7e70e/OceanDNA-b42.fa --refList OceanDNA-b42/target_genomes_gtdb.txt --output OceanDNA-b42/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:27:33,178] [INFO] Task succeeded: fastANI
[2023-03-15 18:27:33,183] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:27:33,184] [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_003697015.1	s__J023 sp003697015	76.2578	219	1315	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	75.4076	107	1315	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525365.1	s__WTGL01 sp011525365	75.2968	61	1315	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837885.1	s__WTGL01 sp009837885	75.1822	64	1315	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCF_006440735.1	s__Mesorhizobium sp006440735	74.7268	51	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204895.1	s__Actinoplanes abujensis	74.6808	101	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003952465.1	s__Mesorhizobium sp003952465	74.6264	63	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.37	98.09	0.92	0.88	6	-
--------------------------------------------------------------------------------
[2023-03-15 18:27:33,184] [INFO] GTDB search result was written to OceanDNA-b42/result_gtdb.tsv
[2023-03-15 18:27:33,184] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:27:33,185] [INFO] DFAST_QC result json was written to OceanDNA-b42/dqc_result.json
[2023-03-15 18:27:33,185] [INFO] DFAST_QC completed!
[2023-03-15 18:27:33,185] [INFO] Total running time: 0h2m25s