[2023-03-17 23:08:31,912] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference
[2023-03-17 23:08:33,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,142] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,142] [INFO] Running command: cat /var/lib/cwl/stg90d6af0a-eb8f-40df-ade3-0fabffe13dce/OceanDNA-b20986.fa | prodigal -d OceanDNA-b20986/cds.fna -a OceanDNA-b20986/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:54,524] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:54,524] [INFO] Task started: HMMsearch
[2023-03-17 23:08:54,524] [INFO] Running command: hmmsearch --tblout OceanDNA-b20986/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/reference_markers.hmm OceanDNA-b20986/protein.faa > /dev/null
[2023-03-17 23:08:54,837] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:54,837] [INFO] Found 6/6 markers.
[2023-03-17 23:08:54,867] [INFO] Query marker FASTA was written to OceanDNA-b20986/markers.fasta
[2023-03-17 23:08:54,868] [INFO] Task started: Blastn
[2023-03-17 23:08:54,868] [INFO] Running command: blastn -query OceanDNA-b20986/markers.fasta -db /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/reference_markers.fasta -out OceanDNA-b20986/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:55,464] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:55,466] [INFO] Selected 43 target genomes.
[2023-03-17 23:08:55,466] [INFO] Target genome list was writen to OceanDNA-b20986/target_genomes.txt
[2023-03-17 23:08:55,485] [INFO] Task started: fastANI
[2023-03-17 23:08:55,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg90d6af0a-eb8f-40df-ade3-0fabffe13dce/OceanDNA-b20986.fa --refList OceanDNA-b20986/target_genomes.txt --output OceanDNA-b20986/fastani_result.tsv --threads 1
[2023-03-17 23:09:30,477] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:30,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:30,477] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:30,484] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:30,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:09:30,484] [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
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.0689	51	1156	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.0273	57	1156	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	74.9453	58	1156	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.9428	82	1156	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	74.917	53	1156	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8571	67	1156	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	74.7688	73	1156	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.7522	59	1156	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	74.575	59	1156	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:09:30,488] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20986/tc_result.tsv
[2023-03-17 23:09:30,489] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:30,489] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:30,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/checkm_data
[2023-03-17 23:09:30,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:30,498] [INFO] Task started: CheckM
[2023-03-17 23:09:30,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20986/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20986/checkm_input OceanDNA-b20986/checkm_result
[2023-03-17 23:10:24,259] [INFO] Task succeeded: CheckM
[2023-03-17 23:10:24,259] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.21%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:10:24,308] [INFO] ===== Completeness check finished =====
[2023-03-17 23:10:24,308] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:10:24,308] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20986/markers.fasta)
[2023-03-17 23:10:24,309] [INFO] Task started: Blastn
[2023-03-17 23:10:24,309] [INFO] Running command: blastn -query OceanDNA-b20986/markers.fasta -db /var/lib/cwl/stg3138c1cd-8721-4a65-a2d7-b45336b2a776/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20986/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:25,190] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:25,211] [INFO] Selected 43 target genomes.
[2023-03-17 23:10:25,211] [INFO] Target genome list was writen to OceanDNA-b20986/target_genomes_gtdb.txt
[2023-03-17 23:10:25,263] [INFO] Task started: fastANI
[2023-03-17 23:10:25,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg90d6af0a-eb8f-40df-ade3-0fabffe13dce/OceanDNA-b20986.fa --refList OceanDNA-b20986/target_genomes_gtdb.txt --output OceanDNA-b20986/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:58,445] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:58,453] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:10:58,453] [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_002841945.1	s__PHBI01 sp002841945	75.7467	130	1156	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226565.1	s__PHBI01 sp006226565	75.7002	137	1156	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526585.1	s__WYBB01 sp011526585	75.4003	103	1156	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792665.1	s__WYBB01 sp016792665	75.2968	94	1156	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001263175.1	s__Vulgatibacter incomptus	75.0689	51	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__Vulgatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780435.1	s__SXOO01 sp018780435	75.0553	71	1156	d__Bacteria;p__Myxococcota;c__UBA9042;o__GCA-2863065;f__GCA-2863065;g__SXOO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903906315.1	s__CAIVJW01 sp903906315	74.8712	73	1156	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	74.8677	62	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793725.1	s__JAEUJP01 sp016793725	74.7901	64	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010894435.1	s__Myxococcus trucidator	74.7522	59	1156	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	74.5695	58	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001528665.1	s__Microtetraspora malaysiensis	74.533	51	1156	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Microtetraspora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:10:58,456] [INFO] GTDB search result was written to OceanDNA-b20986/result_gtdb.tsv
[2023-03-17 23:10:58,464] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:58,470] [INFO] DFAST_QC result json was written to OceanDNA-b20986/dqc_result.json
[2023-03-17 23:10:58,470] [INFO] DFAST_QC completed!
[2023-03-17 23:10:58,470] [INFO] Total running time: 0h2m27s