[2024-01-24 12:23:35,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,019] [INFO] DQC Reference Directory: /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference
[2024-01-24 12:23:36,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,330] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,330] [INFO] Running command: gunzip -c /var/lib/cwl/stg88fe51c5-6cb2-4a64-93db-0509763eff04/GCF_016907515.1_ASM1690751v1_genomic.fna.gz | prodigal -d GCF_016907515.1_ASM1690751v1_genomic.fna/cds.fna -a GCF_016907515.1_ASM1690751v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:51,766] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:51,767] [INFO] Task started: HMMsearch
[2024-01-24 12:23:51,767] [INFO] Running command: hmmsearch --tblout GCF_016907515.1_ASM1690751v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/reference_markers.hmm GCF_016907515.1_ASM1690751v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:52,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:52,017] [INFO] Found 6/6 markers.
[2024-01-24 12:23:52,064] [INFO] Query marker FASTA was written to GCF_016907515.1_ASM1690751v1_genomic.fna/markers.fasta
[2024-01-24 12:23:52,064] [INFO] Task started: Blastn
[2024-01-24 12:23:52,064] [INFO] Running command: blastn -query GCF_016907515.1_ASM1690751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/reference_markers.fasta -out GCF_016907515.1_ASM1690751v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:53,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:53,259] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:53,259] [INFO] Target genome list was writen to GCF_016907515.1_ASM1690751v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:53,264] [INFO] Task started: fastANI
[2024-01-24 12:23:53,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg88fe51c5-6cb2-4a64-93db-0509763eff04/GCF_016907515.1_ASM1690751v1_genomic.fna.gz --refList GCF_016907515.1_ASM1690751v1_genomic.fna/target_genomes.txt --output GCF_016907515.1_ASM1690751v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:10,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:10,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:10,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:10,750] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:10,750] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:10,751] [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 nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	100.0	1937	1938	95	conclusive
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	89.0204	1396	1938	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	88.0577	1200	1938	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	86.7446	1323	1938	95	below_threshold
Nocardioides albidus	strain=CCTCC AB 2015297	GCA_006335005.1	1517589	1517589	type	True	86.5463	1130	1938	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	86.5021	1294	1938	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	86.005	1334	1938	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	85.8713	1361	1938	95	below_threshold
Nocardioides caeni	strain=DSM 23134	GCA_004912195.1	574700	574700	type	True	83.3557	961	1938	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	81.5205	879	1938	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	81.2004	862	1938	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	80.1041	810	1938	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.7813	654	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,752] [INFO] DFAST Taxonomy check result was written to GCF_016907515.1_ASM1690751v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:10,753] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:10,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:10,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/checkm_data
[2024-01-24 12:24:10,754] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:10,804] [INFO] Task started: CheckM
[2024-01-24 12:24:10,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907515.1_ASM1690751v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907515.1_ASM1690751v1_genomic.fna/checkm_input GCF_016907515.1_ASM1690751v1_genomic.fna/checkm_result
[2024-01-24 12:25:29,896] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:29,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:29,918] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:29,918] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:29,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907515.1_ASM1690751v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:29,919] [INFO] Task started: Blastn
[2024-01-24 12:25:29,919] [INFO] Running command: blastn -query GCF_016907515.1_ASM1690751v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb501676f-455a-4754-82dc-6347d2d4f228/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907515.1_ASM1690751v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:31,857] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:31,861] [INFO] Selected 11 target genomes.
[2024-01-24 12:25:31,861] [INFO] Target genome list was writen to GCF_016907515.1_ASM1690751v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:31,867] [INFO] Task started: fastANI
[2024-01-24 12:25:31,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg88fe51c5-6cb2-4a64-93db-0509763eff04/GCF_016907515.1_ASM1690751v1_genomic.fna.gz --refList GCF_016907515.1_ASM1690751v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907515.1_ASM1690751v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:48,249] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:48,258] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:48,258] [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_016907515.1	s__Nocardioides nitrophenolicus	100.0	1937	1938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006715725.1	s__Nocardioides sp006715725	89.4144	1444	1938	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	89.0294	1394	1938	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	88.6946	1330	1938	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	88.0895	1197	1938	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	86.8093	1315	1938	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	86.5397	1131	1938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	85.9795	1295	1938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	85.8701	1361	1938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
GCF_003054165.1	s__Nocardioides sp003054165	84.6223	1157	1938	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912195.1	s__Nocardioides caeni	83.3429	963	1938	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 12:25:48,260] [INFO] GTDB search result was written to GCF_016907515.1_ASM1690751v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:48,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:48,263] [INFO] DFAST_QC result json was written to GCF_016907515.1_ASM1690751v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:48,263] [INFO] DFAST_QC completed!
[2024-01-24 12:25:48,263] [INFO] Total running time: 0h2m13s