[2024-01-24 12:47:22,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:22,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:22,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference
[2024-01-24 12:47:23,453] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:23,454] [INFO] Task started: Prodigal
[2024-01-24 12:47:23,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg7aee84d8-2f95-4974-97d3-12d27c315f7d/GCF_024614185.1_ASM2461418v1_genomic.fna.gz | prodigal -d GCF_024614185.1_ASM2461418v1_genomic.fna/cds.fna -a GCF_024614185.1_ASM2461418v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:41,481] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:41,481] [INFO] Task started: HMMsearch
[2024-01-24 12:47:41,482] [INFO] Running command: hmmsearch --tblout GCF_024614185.1_ASM2461418v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/reference_markers.hmm GCF_024614185.1_ASM2461418v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:41,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:41,853] [INFO] Found 6/6 markers.
[2024-01-24 12:47:41,908] [INFO] Query marker FASTA was written to GCF_024614185.1_ASM2461418v1_genomic.fna/markers.fasta
[2024-01-24 12:47:41,909] [INFO] Task started: Blastn
[2024-01-24 12:47:41,909] [INFO] Running command: blastn -query GCF_024614185.1_ASM2461418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/reference_markers.fasta -out GCF_024614185.1_ASM2461418v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:43,322] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:43,325] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:43,326] [INFO] Target genome list was writen to GCF_024614185.1_ASM2461418v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:43,332] [INFO] Task started: fastANI
[2024-01-24 12:47:43,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aee84d8-2f95-4974-97d3-12d27c315f7d/GCF_024614185.1_ASM2461418v1_genomic.fna.gz --refList GCF_024614185.1_ASM2461418v1_genomic.fna/target_genomes.txt --output GCF_024614185.1_ASM2461418v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:02,253] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:02,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:02,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:02,272] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:02,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:02,272] [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
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	100.0	2089	2089	95	conclusive
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	87.1557	1292	2089	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	86.7721	1126	2089	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	86.6809	1200	2089	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	86.436	1311	2089	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	85.7406	1098	2089	95	below_threshold
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	84.3631	1121	2089	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.1001	815	2089	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.0176	852	2089	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	80.2849	773	2089	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	80.1691	789	2089	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	80.1648	787	2089	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.7289	672	2089	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.5755	610	2089	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:02,274] [INFO] DFAST Taxonomy check result was written to GCF_024614185.1_ASM2461418v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:02,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:02,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:02,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/checkm_data
[2024-01-24 12:48:02,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:02,348] [INFO] Task started: CheckM
[2024-01-24 12:48:02,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024614185.1_ASM2461418v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024614185.1_ASM2461418v1_genomic.fna/checkm_input GCF_024614185.1_ASM2461418v1_genomic.fna/checkm_result
[2024-01-24 12:49:36,673] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:36,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:36,702] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:36,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:36,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024614185.1_ASM2461418v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:36,703] [INFO] Task started: Blastn
[2024-01-24 12:49:36,703] [INFO] Running command: blastn -query GCF_024614185.1_ASM2461418v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e96b909-6182-4eab-9204-a69337910260/dqc_reference/reference_markers_gtdb.fasta -out GCF_024614185.1_ASM2461418v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:38,732] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:38,735] [INFO] Selected 15 target genomes.
[2024-01-24 12:49:38,736] [INFO] Target genome list was writen to GCF_024614185.1_ASM2461418v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:38,790] [INFO] Task started: fastANI
[2024-01-24 12:49:38,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg7aee84d8-2f95-4974-97d3-12d27c315f7d/GCF_024614185.1_ASM2461418v1_genomic.fna.gz --refList GCF_024614185.1_ASM2461418v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024614185.1_ASM2461418v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:57,365] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:57,379] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:49:57,379] [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_006494775.1	s__Nocardioides humi	87.1353	1294	2089	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	86.9728	1257	2089	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	86.8744	1229	2089	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	86.7144	1132	2089	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	86.6513	1203	2089	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	86.4764	1306	2089	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	85.7531	1097	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408525.1	s__Nocardioides aromaticivorans	84.3654	1121	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_001428825.1	s__Nocardioides sp001428825	84.1706	1105	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003054165.1	s__Nocardioides sp003054165	84.1249	1069	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428565.1	s__Nocardioides sp001428565	83.1281	1017	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014108865.1	s__Nocardioides sp014108865	82.1367	965	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	80.3212	767	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014842875.1	s__Nocardioides sp014842875	79.5833	609	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319165.1	s__Nocardioides acrostichi	79.2483	654	2089	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:57,381] [INFO] GTDB search result was written to GCF_024614185.1_ASM2461418v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:57,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:57,385] [INFO] DFAST_QC result json was written to GCF_024614185.1_ASM2461418v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:57,386] [INFO] DFAST_QC completed!
[2024-01-24 12:49:57,386] [INFO] Total running time: 0h2m35s