[2024-01-24 13:01:24,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference
[2024-01-24 13:01:25,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,941] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,941] [INFO] Running command: gunzip -c /var/lib/cwl/stgacdab3a6-02bc-43dc-b282-65022124caaf/GCF_032393075.1_ASM3239307v1_genomic.fna.gz | prodigal -d GCF_032393075.1_ASM3239307v1_genomic.fna/cds.fna -a GCF_032393075.1_ASM3239307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:40,140] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:40,141] [INFO] Task started: HMMsearch
[2024-01-24 13:01:40,141] [INFO] Running command: hmmsearch --tblout GCF_032393075.1_ASM3239307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/reference_markers.hmm GCF_032393075.1_ASM3239307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:40,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:40,404] [INFO] Found 6/6 markers.
[2024-01-24 13:01:40,446] [INFO] Query marker FASTA was written to GCF_032393075.1_ASM3239307v1_genomic.fna/markers.fasta
[2024-01-24 13:01:40,447] [INFO] Task started: Blastn
[2024-01-24 13:01:40,447] [INFO] Running command: blastn -query GCF_032393075.1_ASM3239307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/reference_markers.fasta -out GCF_032393075.1_ASM3239307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:41,717] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:41,720] [INFO] Selected 14 target genomes.
[2024-01-24 13:01:41,721] [INFO] Target genome list was writen to GCF_032393075.1_ASM3239307v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:41,727] [INFO] Task started: fastANI
[2024-01-24 13:01:41,727] [INFO] Running command: fastANI --query /var/lib/cwl/stgacdab3a6-02bc-43dc-b282-65022124caaf/GCF_032393075.1_ASM3239307v1_genomic.fna.gz --refList GCF_032393075.1_ASM3239307v1_genomic.fna/target_genomes.txt --output GCF_032393075.1_ASM3239307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:57,076] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:57,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:57,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:57,095] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:57,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:57,095] [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 kroppenstedtii	strain=DSM 44908	GCA_900111805.1	293050	293050	type	True	97.4734	1231	1384	95	conclusive
Rhodococcus kroppenstedtii	strain=DSM 44908	GCA_001646725.1	293050	293050	type	True	97.4591	1137	1384	95	conclusive
Rhodococcus corynebacterioides	strain=NBRC 14404	GCA_001894765.1	53972	53972	suspected-type	True	91.9216	1211	1384	95	below_threshold
Rhodococcus corynebacterioides	strain=DSM 20151	GCA_001646675.1	53972	53972	suspected-type	True	91.8204	1121	1384	95	below_threshold
Rhodococcus trifolii	strain=CCM 7905	GCA_014635345.1	908250	908250	type	True	79.4368	640	1384	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	79.2566	525	1384	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	79.0221	508	1384	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	78.9912	566	1384	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.9695	551	1384	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	78.9014	554	1384	95	below_threshold
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	78.8412	591	1384	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	78.821	578	1384	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	78.2749	466	1384	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	78.1108	488	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,096] [INFO] DFAST Taxonomy check result was written to GCF_032393075.1_ASM3239307v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:57,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:57,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:57,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/checkm_data
[2024-01-24 13:01:57,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:57,138] [INFO] Task started: CheckM
[2024-01-24 13:01:57,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032393075.1_ASM3239307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032393075.1_ASM3239307v1_genomic.fna/checkm_input GCF_032393075.1_ASM3239307v1_genomic.fna/checkm_result
[2024-01-24 13:02:57,544] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:57,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:57,562] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:57,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:57,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032393075.1_ASM3239307v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:57,563] [INFO] Task started: Blastn
[2024-01-24 13:02:57,564] [INFO] Running command: blastn -query GCF_032393075.1_ASM3239307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99b681b2-9132-4e57-980d-c94cde1bbae8/dqc_reference/reference_markers_gtdb.fasta -out GCF_032393075.1_ASM3239307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:59,394] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:59,399] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:59,399] [INFO] Target genome list was writen to GCF_032393075.1_ASM3239307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:59,411] [INFO] Task started: fastANI
[2024-01-24 13:02:59,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgacdab3a6-02bc-43dc-b282-65022124caaf/GCF_032393075.1_ASM3239307v1_genomic.fna.gz --refList GCF_032393075.1_ASM3239307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032393075.1_ASM3239307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:15,134] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:15,153] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:15,153] [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_900111805.1	s__Rhodococcus_C kroppenstedtii	97.4734	1231	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	98.58	98.00	0.94	0.91	5	conclusive
GCF_001894765.1	s__Rhodococcus_C corynebacterioides	91.9216	1211	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000686025.1	s__Rhodococcus_C sp000686025	81.2828	906	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	97.13	95.65	0.89	0.88	5	-
GCF_001426185.1	s__Rhodococcus_C sp001426185	80.9938	813	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.01	98.03	0.95	0.90	3	-
GCF_014635345.1	s__Rhodococcus_C trifolii	79.4446	639	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	79.28	549	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_000954115.1	s__Rhodococcus_B sp000954115	79.0652	563	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.19	0.90	0.89	13	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.9992	565	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894865.1	s__Rhodococcus maanshanensis	78.9871	540	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_000014565.1	s__Rhodococcus jostii_A	78.9734	606	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_005049235.1	s__Rhodococcus oryzae	78.9651	551	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_002259405.1	s__Rhodococcus_B sp002259405	78.8943	567	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_B	95.0	98.26	98.16	0.87	0.86	5	-
GCF_012726205.1	s__Rhodococcus sp012726205	78.6214	506	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	78.4566	553	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:15,155] [INFO] GTDB search result was written to GCF_032393075.1_ASM3239307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:15,156] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:15,160] [INFO] DFAST_QC result json was written to GCF_032393075.1_ASM3239307v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:15,160] [INFO] DFAST_QC completed!
[2024-01-24 13:03:15,160] [INFO] Total running time: 0h1m51s