[2024-01-24 14:39:15,639] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,641] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,641] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference
[2024-01-24 14:39:18,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:18,587] [INFO] Task started: Prodigal
[2024-01-24 14:39:18,588] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc53e723-50c9-4b39-b4dc-4001d93964ec/GCF_004331345.1_ASM433134v1_genomic.fna.gz | prodigal -d GCF_004331345.1_ASM433134v1_genomic.fna/cds.fna -a GCF_004331345.1_ASM433134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:45,629] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:45,630] [INFO] Task started: HMMsearch
[2024-01-24 14:39:45,630] [INFO] Running command: hmmsearch --tblout GCF_004331345.1_ASM433134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/reference_markers.hmm GCF_004331345.1_ASM433134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:46,032] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:46,034] [INFO] Found 6/6 markers.
[2024-01-24 14:39:46,110] [INFO] Query marker FASTA was written to GCF_004331345.1_ASM433134v1_genomic.fna/markers.fasta
[2024-01-24 14:39:46,110] [INFO] Task started: Blastn
[2024-01-24 14:39:46,110] [INFO] Running command: blastn -query GCF_004331345.1_ASM433134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/reference_markers.fasta -out GCF_004331345.1_ASM433134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:47,346] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:47,349] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:47,350] [INFO] Target genome list was writen to GCF_004331345.1_ASM433134v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:47,382] [INFO] Task started: fastANI
[2024-01-24 14:39:47,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc53e723-50c9-4b39-b4dc-4001d93964ec/GCF_004331345.1_ASM433134v1_genomic.fna.gz --refList GCF_004331345.1_ASM433134v1_genomic.fna/target_genomes.txt --output GCF_004331345.1_ASM433134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:10,271] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:10,271] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:10,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:10,282] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:10,282] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:10,282] [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
Kribbella soli	strain=KCTC 29219	GCA_004331345.1	1124743	1124743	type	True	100.0	2922	2922	95	conclusive
Kribbella sindirgiensis	strain=DSM 27082	GCA_004331435.1	1124744	1124744	type	True	91.9964	2420	2922	95	below_threshold
Kribbella speibonae	strain=YM55	GCA_004331375.1	1572660	1572660	type	True	91.9878	2490	2922	95	below_threshold
Kribbella shirazensis	strain=DSM 45490	GCA_011761605.1	1105143	1105143	type	True	88.2114	2232	2922	95	below_threshold
Kribbella aluminosa	strain=DSM 18824	GCA_017876295.1	416017	416017	type	True	87.219	2100	2922	95	below_threshold
Kribbella jiaozuonensis	strain=NEAU-THZ27	GCA_005233875.1	2575441	2575441	type	True	87.144	2124	2922	95	below_threshold
Kribbella jejuensis	strain=DSM 17305	GCA_006715085.1	236068	236068	type	True	86.7225	1974	2922	95	below_threshold
Kribbella capetownensis	strain=YM53	GCA_004331485.1	1572659	1572659	type	True	84.7112	2010	2922	95	below_threshold
Kribbella turkmenica	strain=16K104	GCA_004348725.1	2530375	2530375	type	True	84.451	1654	2922	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	77.6443	582	2922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:10,284] [INFO] DFAST Taxonomy check result was written to GCF_004331345.1_ASM433134v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:10,285] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:10,285] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:10,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/checkm_data
[2024-01-24 14:40:10,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:10,372] [INFO] Task started: CheckM
[2024-01-24 14:40:10,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004331345.1_ASM433134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004331345.1_ASM433134v1_genomic.fna/checkm_input GCF_004331345.1_ASM433134v1_genomic.fna/checkm_result
[2024-01-24 14:41:30,086] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:30,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:30,114] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:30,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:30,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004331345.1_ASM433134v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:30,115] [INFO] Task started: Blastn
[2024-01-24 14:41:30,115] [INFO] Running command: blastn -query GCF_004331345.1_ASM433134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4733f2e-4674-4f3e-87e2-dbcd615de26e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004331345.1_ASM433134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:32,017] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:32,020] [INFO] Selected 7 target genomes.
[2024-01-24 14:41:32,021] [INFO] Target genome list was writen to GCF_004331345.1_ASM433134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:32,026] [INFO] Task started: fastANI
[2024-01-24 14:41:32,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc53e723-50c9-4b39-b4dc-4001d93964ec/GCF_004331345.1_ASM433134v1_genomic.fna.gz --refList GCF_004331345.1_ASM433134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004331345.1_ASM433134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:49,623] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:49,635] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:49,635] [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_004331345.1	s__Kribbella soli	100.0	2922	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004216905.1	s__Kribbella sp004216905	93.8256	2495	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366075.1	s__Kribbella sp004366075	92.9368	2393	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	97.22	95.50	0.92	0.87	3	-
GCF_004331435.1	s__Kribbella sindirgiensis	91.9866	2422	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	95.59	95.53	0.88	0.88	3	-
GCF_011761605.1	s__Kribbella shirazensis	88.2169	2231	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876295.1	s__Kribbella aluminosa	87.2211	2100	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005233875.1	s__Kribbella sp005233875	87.1372	2123	2922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Kribbellaceae;g__Kribbella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:49,636] [INFO] GTDB search result was written to GCF_004331345.1_ASM433134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:49,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:49,640] [INFO] DFAST_QC result json was written to GCF_004331345.1_ASM433134v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:49,640] [INFO] DFAST_QC completed!
[2024-01-24 14:41:49,640] [INFO] Total running time: 0h2m34s