[2024-01-24 14:19:31,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,773] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference
[2024-01-24 14:19:33,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,010] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,010] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb95ced7-8773-47e6-9ab7-b79acd5073b0/GCF_006538965.1_ASM653896v1_genomic.fna.gz | prodigal -d GCF_006538965.1_ASM653896v1_genomic.fna/cds.fna -a GCF_006538965.1_ASM653896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:47,224] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:47,225] [INFO] Task started: HMMsearch
[2024-01-24 14:19:47,225] [INFO] Running command: hmmsearch --tblout GCF_006538965.1_ASM653896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/reference_markers.hmm GCF_006538965.1_ASM653896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:47,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:47,613] [INFO] Found 6/6 markers.
[2024-01-24 14:19:47,678] [INFO] Query marker FASTA was written to GCF_006538965.1_ASM653896v1_genomic.fna/markers.fasta
[2024-01-24 14:19:47,678] [INFO] Task started: Blastn
[2024-01-24 14:19:47,678] [INFO] Running command: blastn -query GCF_006538965.1_ASM653896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/reference_markers.fasta -out GCF_006538965.1_ASM653896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:49,063] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:49,066] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:49,067] [INFO] Target genome list was writen to GCF_006538965.1_ASM653896v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:49,088] [INFO] Task started: fastANI
[2024-01-24 14:19:49,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb95ced7-8773-47e6-9ab7-b79acd5073b0/GCF_006538965.1_ASM653896v1_genomic.fna.gz --refList GCF_006538965.1_ASM653896v1_genomic.fna/target_genomes.txt --output GCF_006538965.1_ASM653896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:08,390] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:08,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:08,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:08,402] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:08,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:08,402] [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
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	100.0	1850	1854	95	conclusive
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	99.9865	1853	1854	95	conclusive
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	85.9625	1323	1854	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	85.7243	1264	1854	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	85.6691	1122	1854	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	85.6306	1244	1854	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	85.5799	1255	1854	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	84.9555	1163	1854	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	84.9074	1045	1854	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.4226	858	1854	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.2169	839	1854	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.1314	708	1854	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.7876	624	1854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,404] [INFO] DFAST Taxonomy check result was written to GCF_006538965.1_ASM653896v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:08,405] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:08,405] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:08,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/checkm_data
[2024-01-24 14:20:08,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:08,465] [INFO] Task started: CheckM
[2024-01-24 14:20:08,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006538965.1_ASM653896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006538965.1_ASM653896v1_genomic.fna/checkm_input GCF_006538965.1_ASM653896v1_genomic.fna/checkm_result
[2024-01-24 14:21:20,649] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:20,650] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:20,670] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:20,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:20,671] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006538965.1_ASM653896v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:20,672] [INFO] Task started: Blastn
[2024-01-24 14:21:20,672] [INFO] Running command: blastn -query GCF_006538965.1_ASM653896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5e96bed-b79a-40a7-92a2-d2f204eb4da3/dqc_reference/reference_markers_gtdb.fasta -out GCF_006538965.1_ASM653896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:22,723] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:22,726] [INFO] Selected 10 target genomes.
[2024-01-24 14:21:22,726] [INFO] Target genome list was writen to GCF_006538965.1_ASM653896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:22,756] [INFO] Task started: fastANI
[2024-01-24 14:21:22,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb95ced7-8773-47e6-9ab7-b79acd5073b0/GCF_006538965.1_ASM653896v1_genomic.fna.gz --refList GCF_006538965.1_ASM653896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006538965.1_ASM653896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:38,273] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:38,282] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:38,282] [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_900114845.1	s__Nocardioides simplex	99.9865	1853	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	conclusive
GCF_018831735.1	s__Nocardioides sp018831735	91.2228	1532	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	85.946	1325	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	85.8774	1300	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	85.7754	1222	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	85.6394	1125	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494775.1	s__Nocardioides humi	85.5959	1248	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409625.1	s__Nocardioides kongjuensis	85.5798	1255	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335005.1	s__Nocardioides albidus	84.9392	1042	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428825.1	s__Nocardioides sp001428825	84.7962	1149	1854	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:38,284] [INFO] GTDB search result was written to GCF_006538965.1_ASM653896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:38,284] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:38,287] [INFO] DFAST_QC result json was written to GCF_006538965.1_ASM653896v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:38,287] [INFO] DFAST_QC completed!
[2024-01-24 14:21:38,287] [INFO] Total running time: 0h2m7s