[2024-01-24 14:14:05,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:05,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:05,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference
[2024-01-24 14:14:07,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:07,211] [INFO] Task started: Prodigal
[2024-01-24 14:14:07,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a4f7ed1-48bc-4022-83a9-e11dcc8f87d7/GCF_001189295.1_ASM118929v1_genomic.fna.gz | prodigal -d GCF_001189295.1_ASM118929v1_genomic.fna/cds.fna -a GCF_001189295.1_ASM118929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:45,646] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:45,647] [INFO] Task started: HMMsearch
[2024-01-24 14:14:45,647] [INFO] Running command: hmmsearch --tblout GCF_001189295.1_ASM118929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/reference_markers.hmm GCF_001189295.1_ASM118929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:46,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:46,076] [INFO] Found 6/6 markers.
[2024-01-24 14:14:46,164] [INFO] Query marker FASTA was written to GCF_001189295.1_ASM118929v1_genomic.fna/markers.fasta
[2024-01-24 14:14:46,164] [INFO] Task started: Blastn
[2024-01-24 14:14:46,165] [INFO] Running command: blastn -query GCF_001189295.1_ASM118929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/reference_markers.fasta -out GCF_001189295.1_ASM118929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:46,910] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:46,913] [INFO] Selected 21 target genomes.
[2024-01-24 14:14:46,913] [INFO] Target genome list was writen to GCF_001189295.1_ASM118929v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:46,937] [INFO] Task started: fastANI
[2024-01-24 14:14:46,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4f7ed1-48bc-4022-83a9-e11dcc8f87d7/GCF_001189295.1_ASM118929v1_genomic.fna.gz --refList GCF_001189295.1_ASM118929v1_genomic.fna/target_genomes.txt --output GCF_001189295.1_ASM118929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:14,547] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:14,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:14,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:14,572] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:14,572] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:14,572] [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
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	100.0	3796	3796	95	conclusive
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	76.9376	968	3796	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	76.8761	862	3796	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	76.7646	921	3796	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.7752	407	3796	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.2025	620	3796	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	75.1434	109	3796	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	75.0671	111	3796	95	below_threshold
Bradyrhizobium niftali	strain=CNPSo 3448	GCA_004571025.1	2560055	2560055	type	True	75.0216	188	3796	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA110	GCA_000011365.1	1355477	1355477	type	True	74.9728	168	3796	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.9483	131	3796	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	74.9445	168	3796	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	74.9049	186	3796	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	74.8705	96	3796	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	74.8579	186	3796	95	below_threshold
Microlunatus speluncae	strain=SYSU K12189	GCA_009299835.1	2594267	2594267	type	True	74.8212	163	3796	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	74.8021	80	3796	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	74.7965	138	3796	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	74.7587	125	3796	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	74.7176	147	3796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,574] [INFO] DFAST Taxonomy check result was written to GCF_001189295.1_ASM118929v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:14,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:14,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:14,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/checkm_data
[2024-01-24 14:15:14,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:14,690] [INFO] Task started: CheckM
[2024-01-24 14:15:14,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001189295.1_ASM118929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001189295.1_ASM118929v1_genomic.fna/checkm_input GCF_001189295.1_ASM118929v1_genomic.fna/checkm_result
[2024-01-24 14:19:55,063] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:55,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:55,095] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:55,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:55,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001189295.1_ASM118929v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:55,098] [INFO] Task started: Blastn
[2024-01-24 14:19:55,098] [INFO] Running command: blastn -query GCF_001189295.1_ASM118929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f32caa2-de0e-4aef-b46f-c00637835f89/dqc_reference/reference_markers_gtdb.fasta -out GCF_001189295.1_ASM118929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:56,376] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:56,379] [INFO] Selected 14 target genomes.
[2024-01-24 14:19:56,380] [INFO] Target genome list was writen to GCF_001189295.1_ASM118929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:56,395] [INFO] Task started: fastANI
[2024-01-24 14:19:56,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4f7ed1-48bc-4022-83a9-e11dcc8f87d7/GCF_001189295.1_ASM118929v1_genomic.fna.gz --refList GCF_001189295.1_ASM118929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001189295.1_ASM118929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:28,800] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:28,822] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:28,823] [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
GCF_001189295.1	s__Chondromyces crocatus	100.0	3795	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000601485.1	s__Chondromyces apiculatus	80.9065	2197	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Chondromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	77.2488	1093	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	77.1457	1066	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	77.0533	1210	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCF_002950945.1	s__Sorangium cellulosum_E	76.9679	1179	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	76.8789	859	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144585.1	s__Polyangium fumosum	76.7691	918	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719945.1	s__CAITIQ01 sp016719945	75.9867	560	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	99.43	99.43	0.95	0.95	2	-
GCA_013361525.1	s__CAITIQ01 sp013361525	75.8546	483	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITIQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858055.1	s__CAIQDA01 sp903858055	75.3105	186	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIQDA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235365.1	s__SZUA-265 sp003235365	75.0075	163	3796	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__SZUA-265	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:28,824] [INFO] GTDB search result was written to GCF_001189295.1_ASM118929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:28,825] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:28,829] [INFO] DFAST_QC result json was written to GCF_001189295.1_ASM118929v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:28,830] [INFO] DFAST_QC completed!
[2024-01-24 14:20:28,830] [INFO] Total running time: 0h6m23s