[2024-01-24 14:31:15,023] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:15,025] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:15,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference
[2024-01-24 14:31:16,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,480] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,480] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaca5847-89df-4f32-8172-b352163b448f/GCF_002865585.1_ASM286558v1_genomic.fna.gz | prodigal -d GCF_002865585.1_ASM286558v1_genomic.fna/cds.fna -a GCF_002865585.1_ASM286558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:28,584] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:28,585] [INFO] Task started: HMMsearch
[2024-01-24 14:31:28,585] [INFO] Running command: hmmsearch --tblout GCF_002865585.1_ASM286558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/reference_markers.hmm GCF_002865585.1_ASM286558v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:28,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:28,937] [INFO] Found 6/6 markers.
[2024-01-24 14:31:28,970] [INFO] Query marker FASTA was written to GCF_002865585.1_ASM286558v1_genomic.fna/markers.fasta
[2024-01-24 14:31:28,970] [INFO] Task started: Blastn
[2024-01-24 14:31:28,970] [INFO] Running command: blastn -query GCF_002865585.1_ASM286558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/reference_markers.fasta -out GCF_002865585.1_ASM286558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:30,361] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:30,364] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:30,364] [INFO] Target genome list was writen to GCF_002865585.1_ASM286558v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:30,374] [INFO] Task started: fastANI
[2024-01-24 14:31:30,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaca5847-89df-4f32-8172-b352163b448f/GCF_002865585.1_ASM286558v1_genomic.fna.gz --refList GCF_002865585.1_ASM286558v1_genomic.fna/target_genomes.txt --output GCF_002865585.1_ASM286558v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:52,421] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:52,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:52,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:52,439] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:52,440] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:52,441] [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 houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	100.0	1280	1280	95	conclusive
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	82.4304	805	1280	95	below_threshold
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	81.22	652	1280	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	80.9775	649	1280	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	80.9572	635	1280	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	80.9548	581	1280	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.9449	620	1280	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	80.888	642	1280	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.7656	661	1280	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	80.6908	654	1280	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	80.6483	600	1280	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.5999	634	1280	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.5625	632	1280	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	80.5474	586	1280	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.4813	569	1280	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.3941	625	1280	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.3553	638	1280	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	80.3028	612	1280	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.2674	607	1280	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.2251	635	1280	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	80.213	663	1280	95	below_threshold
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	79.6843	569	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:52,442] [INFO] DFAST Taxonomy check result was written to GCF_002865585.1_ASM286558v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:52,443] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:52,443] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:52,443] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/checkm_data
[2024-01-24 14:31:52,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:52,485] [INFO] Task started: CheckM
[2024-01-24 14:31:52,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002865585.1_ASM286558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002865585.1_ASM286558v1_genomic.fna/checkm_input GCF_002865585.1_ASM286558v1_genomic.fna/checkm_result
[2024-01-24 14:32:57,660] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:57,662] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:57,682] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:57,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:57,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002865585.1_ASM286558v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:57,684] [INFO] Task started: Blastn
[2024-01-24 14:32:57,684] [INFO] Running command: blastn -query GCF_002865585.1_ASM286558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7ede1909-9a9c-45ef-9c83-f5ccf9c73c70/dqc_reference/reference_markers_gtdb.fasta -out GCF_002865585.1_ASM286558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:59,629] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:59,633] [INFO] Selected 16 target genomes.
[2024-01-24 14:32:59,633] [INFO] Target genome list was writen to GCF_002865585.1_ASM286558v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:59,649] [INFO] Task started: fastANI
[2024-01-24 14:32:59,650] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaca5847-89df-4f32-8172-b352163b448f/GCF_002865585.1_ASM286558v1_genomic.fna.gz --refList GCF_002865585.1_ASM286558v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002865585.1_ASM286558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:33:14,316] [INFO] Task succeeded: fastANI
[2024-01-24 14:33:14,335] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:33:14,335] [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_002865585.1	s__Nocardioides houyundeii	100.0	1280	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.48	96.00	0.92	0.88	3	conclusive
GCF_013624435.2	s__Nocardioides sp013624415	83.1467	909	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_003194625.1	s__Nocardioides solisilvae	82.4602	802	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155365.1	s__Nocardioides sp013155365	81.0114	691	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	80.9778	565	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047265.1	s__Nocardioides terrigena	80.974	633	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_003047295.1	s__Nocardioides sediminis	80.9571	651	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.9382	618	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006007965.1	s__Nocardioides sp006007965	80.8794	643	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001429625.1	s__Nocardioides sp001429625	80.7827	674	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047285.1	s__Nocardioides allogilvus	80.6485	600	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCF_013466985.1	s__Nocardioides ungokensis	80.5563	635	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003057875.1	s__Nocardioides currus	80.4728	655	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.2481	609	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815725.1	s__Nocardioides sp013815725	80.2468	383	1280	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121585.1	s__Nocardioides speluncae	79.6668	571	1280	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 14:33:14,337] [INFO] GTDB search result was written to GCF_002865585.1_ASM286558v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:33:14,337] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:33:14,341] [INFO] DFAST_QC result json was written to GCF_002865585.1_ASM286558v1_genomic.fna/dqc_result.json
[2024-01-24 14:33:14,341] [INFO] DFAST_QC completed!
[2024-01-24 14:33:14,342] [INFO] Total running time: 0h1m59s