[2024-01-24 13:46:25,664] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,665] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,665] [INFO] DQC Reference Directory: /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference
[2024-01-24 13:46:28,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:28,614] [INFO] Task started: Prodigal
[2024-01-24 13:46:28,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8c55e31-303a-487f-bab1-f30e55b4dc4e/GCF_014217785.1_ASM1421778v1_genomic.fna.gz | prodigal -d GCF_014217785.1_ASM1421778v1_genomic.fna/cds.fna -a GCF_014217785.1_ASM1421778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:57,695] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:57,695] [INFO] Task started: HMMsearch
[2024-01-24 13:46:57,695] [INFO] Running command: hmmsearch --tblout GCF_014217785.1_ASM1421778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/reference_markers.hmm GCF_014217785.1_ASM1421778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:57,917] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:57,918] [INFO] Found 6/6 markers.
[2024-01-24 13:46:57,958] [INFO] Query marker FASTA was written to GCF_014217785.1_ASM1421778v1_genomic.fna/markers.fasta
[2024-01-24 13:46:57,958] [INFO] Task started: Blastn
[2024-01-24 13:46:57,958] [INFO] Running command: blastn -query GCF_014217785.1_ASM1421778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/reference_markers.fasta -out GCF_014217785.1_ASM1421778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:59,080] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:59,083] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:59,083] [INFO] Target genome list was writen to GCF_014217785.1_ASM1421778v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:59,141] [INFO] Task started: fastANI
[2024-01-24 13:46:59,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c55e31-303a-487f-bab1-f30e55b4dc4e/GCF_014217785.1_ASM1421778v1_genomic.fna.gz --refList GCF_014217785.1_ASM1421778v1_genomic.fna/target_genomes.txt --output GCF_014217785.1_ASM1421778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:16,142] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:16,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:16,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:16,152] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:47:16,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:16,152] [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
Rhodococcus triatomae	strain=DSM 44892	GCA_014217785.1	300028	300028	type	True	100.0	1590	1590	95	conclusive
Rhodococcus triatomae	strain=DSM 44892	GCA_900099725.1	300028	300028	type	True	99.9753	1562	1590	95	conclusive
Rhodococcus triatomae	strain=NBRC 103116	GCA_001894965.1	300028	300028	type	True	99.9721	1552	1590	95	conclusive
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	79.8399	833	1590	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	79.8034	792	1590	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	79.6155	677	1590	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	79.5992	765	1590	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	79.5462	718	1590	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	79.5283	698	1590	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	79.5227	675	1590	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	79.42	674	1590	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	79.4155	694	1590	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	79.3641	707	1590	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	79.3636	711	1590	95	below_threshold
Rhodococcus kroppenstedtii	strain=DSM 44908	GCA_001646725.1	293050	293050	type	True	78.6835	468	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:16,154] [INFO] DFAST Taxonomy check result was written to GCF_014217785.1_ASM1421778v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:16,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:16,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:16,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/checkm_data
[2024-01-24 13:47:16,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:16,200] [INFO] Task started: CheckM
[2024-01-24 13:47:16,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014217785.1_ASM1421778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014217785.1_ASM1421778v1_genomic.fna/checkm_input GCF_014217785.1_ASM1421778v1_genomic.fna/checkm_result
[2024-01-24 13:48:54,241] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:54,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:54,258] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:54,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:54,258] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014217785.1_ASM1421778v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:54,258] [INFO] Task started: Blastn
[2024-01-24 13:48:54,258] [INFO] Running command: blastn -query GCF_014217785.1_ASM1421778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg308909b4-4372-49c1-ac1e-86613ba9e11a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014217785.1_ASM1421778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:55,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:55,932] [INFO] Selected 19 target genomes.
[2024-01-24 13:48:55,932] [INFO] Target genome list was writen to GCF_014217785.1_ASM1421778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:56,002] [INFO] Task started: fastANI
[2024-01-24 13:48:56,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8c55e31-303a-487f-bab1-f30e55b4dc4e/GCF_014217785.1_ASM1421778v1_genomic.fna.gz --refList GCF_014217785.1_ASM1421778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014217785.1_ASM1421778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:19,540] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:19,551] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:19,551] [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_014217785.1	s__Rhodococcus triatomae	100.0	1590	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	4	conclusive
GCF_012726205.1	s__Rhodococcus sp012726205	79.8848	720	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010805.1	s__Rhodococcus opacus_C	79.853	807	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068395.1	s__Rhodococcus sp002165735	79.8203	835	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	79.7255	799	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
GCF_000014565.1	s__Rhodococcus jostii_A	79.6756	812	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_012396235.1	s__Rhodococcus opacus	79.6674	774	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
GCF_014256275.1	s__Rhodococcus wratislaviensis_A	79.656	806	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900105905.1	s__Rhodococcus koreensis	79.6377	828	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.00	98.46	0.87	0.80	4	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	79.5845	681	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004011865.1	s__Rhodococcus agglutinans	79.5702	715	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	79.5613	705	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_001646645.1	s__Rhodococcus hoagii	79.5142	625	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_005484805.1	s__Rhodococcus sp005484805	79.4904	701	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894925.1	s__Rhodococcus rhodnii	79.3867	667	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	0.99	0.98	3	-
GCF_011058165.1	s__Rhodococcus aetherivorans	79.3098	719	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	78.2342	519	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_001613365.1	s__Nocardia xishanensis	78.0063	534	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123685.1	s__Nocardia aurea	77.8627	478	1590	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:19,553] [INFO] GTDB search result was written to GCF_014217785.1_ASM1421778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:19,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:19,556] [INFO] DFAST_QC result json was written to GCF_014217785.1_ASM1421778v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:19,556] [INFO] DFAST_QC completed!
[2024-01-24 13:49:19,557] [INFO] Total running time: 0h2m54s