[2023-06-29 12:09:41,870] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:09:41,872] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:09:41,872] [INFO] DQC Reference Directory: /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference
[2023-06-29 12:09:43,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:09:43,161] [INFO] Task started: Prodigal
[2023-06-29 12:09:43,161] [INFO] Running command: gunzip -c /var/lib/cwl/stga895ad1f-5aeb-4635-be18-b4e02343a894/GCA_020439785.1_ASM2043978v1_genomic.fna.gz | prodigal -d GCA_020439785.1_ASM2043978v1_genomic.fna/cds.fna -a GCA_020439785.1_ASM2043978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:09:54,603] [INFO] Task succeeded: Prodigal
[2023-06-29 12:09:54,604] [INFO] Task started: HMMsearch
[2023-06-29 12:09:54,604] [INFO] Running command: hmmsearch --tblout GCA_020439785.1_ASM2043978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/reference_markers.hmm GCA_020439785.1_ASM2043978v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:09:54,899] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:09:54,900] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga895ad1f-5aeb-4635-be18-b4e02343a894/GCA_020439785.1_ASM2043978v1_genomic.fna.gz]
[2023-06-29 12:09:54,960] [INFO] Query marker FASTA was written to GCA_020439785.1_ASM2043978v1_genomic.fna/markers.fasta
[2023-06-29 12:09:54,960] [INFO] Task started: Blastn
[2023-06-29 12:09:54,960] [INFO] Running command: blastn -query GCA_020439785.1_ASM2043978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/reference_markers.fasta -out GCA_020439785.1_ASM2043978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:09:55,613] [INFO] Task succeeded: Blastn
[2023-06-29 12:09:55,617] [INFO] Selected 25 target genomes.
[2023-06-29 12:09:55,617] [INFO] Target genome list was writen to GCA_020439785.1_ASM2043978v1_genomic.fna/target_genomes.txt
[2023-06-29 12:09:55,749] [INFO] Task started: fastANI
[2023-06-29 12:09:55,749] [INFO] Running command: fastANI --query /var/lib/cwl/stga895ad1f-5aeb-4635-be18-b4e02343a894/GCA_020439785.1_ASM2043978v1_genomic.fna.gz --refList GCA_020439785.1_ASM2043978v1_genomic.fna/target_genomes.txt --output GCA_020439785.1_ASM2043978v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:10:16,161] [INFO] Task succeeded: fastANI
[2023-06-29 12:10:16,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:10:16,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:10:16,182] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:10:16,182] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:10:16,182] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.2131	54	1202	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	75.0043	66	1202	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	74.9907	68	1202	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	74.9856	50	1202	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	74.8683	60	1202	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	74.8652	52	1202	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	74.8648	58	1202	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	74.8371	64	1202	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	74.8148	76	1202	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	74.8036	98	1202	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	74.7819	53	1202	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	74.777	54	1202	95	below_threshold
Herbidospora cretacea	strain=NBRC 15474	GCA_001570605.1	28444	28444	type	True	74.6894	90	1202	95	below_threshold
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	74.6612	74	1202	95	below_threshold
Sphaerisporangium rufum	strain=NBRC 109079	GCA_016863395.1	1381558	1381558	type	True	74.6071	81	1202	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	74.579	83	1202	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	74.5709	56	1202	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:10:16,184] [INFO] DFAST Taxonomy check result was written to GCA_020439785.1_ASM2043978v1_genomic.fna/tc_result.tsv
[2023-06-29 12:10:16,185] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:10:16,185] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:10:16,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/checkm_data
[2023-06-29 12:10:16,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:10:16,232] [INFO] Task started: CheckM
[2023-06-29 12:10:16,233] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020439785.1_ASM2043978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020439785.1_ASM2043978v1_genomic.fna/checkm_input GCA_020439785.1_ASM2043978v1_genomic.fna/checkm_result
[2023-06-29 12:10:51,498] [INFO] Task succeeded: CheckM
[2023-06-29 12:10:51,499] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.55%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-29 12:10:51,525] [INFO] ===== Completeness check finished =====
[2023-06-29 12:10:51,525] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:10:51,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020439785.1_ASM2043978v1_genomic.fna/markers.fasta)
[2023-06-29 12:10:51,526] [INFO] Task started: Blastn
[2023-06-29 12:10:51,526] [INFO] Running command: blastn -query GCA_020439785.1_ASM2043978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd234799f-af48-442a-8cee-5c5e3bab37c0/dqc_reference/reference_markers_gtdb.fasta -out GCA_020439785.1_ASM2043978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:10:52,486] [INFO] Task succeeded: Blastn
[2023-06-29 12:10:52,491] [INFO] Selected 28 target genomes.
[2023-06-29 12:10:52,491] [INFO] Target genome list was writen to GCA_020439785.1_ASM2043978v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:10:52,506] [INFO] Task started: fastANI
[2023-06-29 12:10:52,506] [INFO] Running command: fastANI --query /var/lib/cwl/stga895ad1f-5aeb-4635-be18-b4e02343a894/GCA_020439785.1_ASM2043978v1_genomic.fna.gz --refList GCA_020439785.1_ASM2043978v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020439785.1_ASM2043978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:11:12,465] [INFO] Task succeeded: fastANI
[2023-06-29 12:11:12,481] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:11:12,482] [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_016125275.1	s__RI-231 sp016125275	78.0151	492	1202	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__UBA6623;g__RI-231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871015.1	s__SYLY01 sp016871015	75.7753	84	1202	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859945.1	s__Pseudobythopirellula maris	75.2131	54	1202	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.0795	86	1202	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298115.1	s__RBG-13-68-16 sp004298115	74.9818	63	1202	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425465.1	s__Methylobacterium sp001425465	74.9542	68	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106665.1	s__Paracoccus sanguinis	74.86	61	1202	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.10	96.00	0.89	0.81	6	-
GCF_001293525.1	s__Ideonella_A sakaiensis	74.8502	115	1202	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	74.8026	65	1202	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_016209145.1	s__JACQWT01 sp016209145	74.7442	89	1202	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JACQWT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218785.1	s__JACRCY01 sp016218785	74.7268	62	1202	d__Bacteria;p__Myxococcota;c__Polyangia;o__JACRCY01;f__JACRCY01;g__JACRCY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016863395.1	s__Sphaerisporangium rufum	74.6116	82	1202	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:11:12,483] [INFO] GTDB search result was written to GCA_020439785.1_ASM2043978v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:11:12,484] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:11:12,488] [INFO] DFAST_QC result json was written to GCA_020439785.1_ASM2043978v1_genomic.fna/dqc_result.json
[2023-06-29 12:11:12,488] [INFO] DFAST_QC completed!
[2023-06-29 12:11:12,488] [INFO] Total running time: 0h1m31s