[2024-01-24 13:58:10,721] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,725] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,725] [INFO] DQC Reference Directory: /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference
[2024-01-24 13:58:12,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,104] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg431089b7-22e9-4586-9b5a-98427aa6240b/GCF_008373765.1_ASM837376v1_genomic.fna.gz | prodigal -d GCF_008373765.1_ASM837376v1_genomic.fna/cds.fna -a GCF_008373765.1_ASM837376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,277] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,277] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,278] [INFO] Running command: hmmsearch --tblout GCF_008373765.1_ASM837376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/reference_markers.hmm GCF_008373765.1_ASM837376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:24,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:24,554] [INFO] Found 6/6 markers.
[2024-01-24 13:58:24,597] [INFO] Query marker FASTA was written to GCF_008373765.1_ASM837376v1_genomic.fna/markers.fasta
[2024-01-24 13:58:24,597] [INFO] Task started: Blastn
[2024-01-24 13:58:24,598] [INFO] Running command: blastn -query GCF_008373765.1_ASM837376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/reference_markers.fasta -out GCF_008373765.1_ASM837376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:25,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:25,919] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:25,920] [INFO] Target genome list was writen to GCF_008373765.1_ASM837376v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:25,936] [INFO] Task started: fastANI
[2024-01-24 13:58:25,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg431089b7-22e9-4586-9b5a-98427aa6240b/GCF_008373765.1_ASM837376v1_genomic.fna.gz --refList GCF_008373765.1_ASM837376v1_genomic.fna/target_genomes.txt --output GCF_008373765.1_ASM837376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:43,823] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:43,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:43,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:43,840] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:43,841] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:43,841] [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 antri	strain=BN140041	GCA_008373765.1	2607659	2607659	type	True	100.0	1358	1358	95	conclusive
Nocardioides immobilis	strain=CCTCC AB 2017083	GCA_003515065.1	2049295	2049295	type	True	86.1482	1080	1358	95	below_threshold
Nocardioides pelophilus	strain=CGMCC 4.7388	GCA_014180685.1	2172019	2172019	type	True	85.5484	900	1358	95	below_threshold
Nocardioides silvaticus	strain=CCTCC AB 2018079	GCA_003160695.1	2201891	2201891	type	True	84.7927	966	1358	95	below_threshold
Nocardioides stalactiti	strain=1.0914	GCA_014180715.1	2755356	2755356	type	True	84.0613	874	1358	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	83.4287	949	1358	95	below_threshold
Nocardioides thalensis	strain=DSM 103833	GCA_013410655.1	1914755	1914755	type	True	82.6969	879	1358	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	81.752	835	1358	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	81.4547	798	1358	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.8709	726	1358	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	80.7085	682	1358	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.4005	734	1358	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	80.3797	745	1358	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.0353	649	1358	95	below_threshold
Nocardioides coralli	strain=SCSIO 67246	GCA_019880385.1	2872154	2872154	type	True	79.9332	584	1358	95	below_threshold
Nocardioides acrostichi	strain=CBS4Y-1	GCA_015319165.1	2784339	2784339	type	True	79.5666	570	1358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,842] [INFO] DFAST Taxonomy check result was written to GCF_008373765.1_ASM837376v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:43,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:43,843] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:43,843] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/checkm_data
[2024-01-24 13:58:43,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:43,886] [INFO] Task started: CheckM
[2024-01-24 13:58:43,887] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008373765.1_ASM837376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008373765.1_ASM837376v1_genomic.fna/checkm_input GCF_008373765.1_ASM837376v1_genomic.fna/checkm_result
[2024-01-24 13:59:38,180] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:38,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:38,203] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:38,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:38,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008373765.1_ASM837376v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:38,204] [INFO] Task started: Blastn
[2024-01-24 13:59:38,204] [INFO] Running command: blastn -query GCF_008373765.1_ASM837376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb65fc221-5e42-4eed-9520-370b6d6ca1e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_008373765.1_ASM837376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:40,057] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:40,061] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:40,062] [INFO] Target genome list was writen to GCF_008373765.1_ASM837376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:40,088] [INFO] Task started: fastANI
[2024-01-24 13:59:40,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg431089b7-22e9-4586-9b5a-98427aa6240b/GCF_008373765.1_ASM837376v1_genomic.fna.gz --refList GCF_008373765.1_ASM837376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008373765.1_ASM837376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:54,549] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:54,566] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:54,566] [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_008373765.1	s__Nocardioides antri	100.0	1358	1358	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_003515065.1	s__Nocardioides immobilis	86.1133	1083	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180685.1	s__Nocardioides pelophilus	85.5241	902	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003160695.1	s__Nocardioides silvaticus	84.7954	966	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014180715.1	s__Nocardioides stalactiti	84.0835	872	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008373755.1	s__Nocardioides sp008373755	83.4175	951	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519005.1	s__Nocardioides sp000519005	81.9005	809	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.89	98.89	0.90	0.90	2	-
GCF_006494775.1	s__Nocardioides humi	81.7095	840	1358	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	81.0937	770	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006494815.1	s__Nocardioides sambongensis	80.8667	726	1358	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	80.795	746	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	80.6461	688	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	80.4263	729	1358	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:54,568] [INFO] GTDB search result was written to GCF_008373765.1_ASM837376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:54,569] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:54,573] [INFO] DFAST_QC result json was written to GCF_008373765.1_ASM837376v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:54,573] [INFO] DFAST_QC completed!
[2024-01-24 13:59:54,574] [INFO] Total running time: 0h1m44s