[2024-01-24 12:29:29,037] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:29,038] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:29,039] [INFO] DQC Reference Directory: /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference
[2024-01-24 12:29:30,475] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,475] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg7625892d-bd4a-44a1-b868-14a01e717bee/GCF_006704125.1_ASM670412v1_genomic.fna.gz | prodigal -d GCF_006704125.1_ASM670412v1_genomic.fna/cds.fna -a GCF_006704125.1_ASM670412v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:47,182] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:47,183] [INFO] Task started: HMMsearch
[2024-01-24 12:29:47,183] [INFO] Running command: hmmsearch --tblout GCF_006704125.1_ASM670412v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/reference_markers.hmm GCF_006704125.1_ASM670412v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:47,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:47,560] [INFO] Found 6/6 markers.
[2024-01-24 12:29:47,618] [INFO] Query marker FASTA was written to GCF_006704125.1_ASM670412v1_genomic.fna/markers.fasta
[2024-01-24 12:29:47,618] [INFO] Task started: Blastn
[2024-01-24 12:29:47,618] [INFO] Running command: blastn -query GCF_006704125.1_ASM670412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/reference_markers.fasta -out GCF_006704125.1_ASM670412v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:49,023] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:49,026] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:49,026] [INFO] Target genome list was writen to GCF_006704125.1_ASM670412v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:49,033] [INFO] Task started: fastANI
[2024-01-24 12:29:49,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg7625892d-bd4a-44a1-b868-14a01e717bee/GCF_006704125.1_ASM670412v1_genomic.fna.gz --refList GCF_006704125.1_ASM670412v1_genomic.fna/target_genomes.txt --output GCF_006704125.1_ASM670412v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:07,362] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:07,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:07,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:07,377] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:07,377] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:07,377] [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 spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	100.0	1591	1593	95	conclusive
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	83.5889	1144	1593	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	83.561	1133	1593	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	83.0925	1108	1593	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	83.0553	1143	1593	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	83.048	1128	1593	95	below_threshold
Prescottella subtropica	strain=C9-28	GCA_005434945.1	2545757	2545757	type	True	80.9073	772	1593	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	80.8665	911	1593	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	80.7928	821	1593	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	80.0377	774	1593	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	79.895	795	1593	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	79.8424	724	1593	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	79.8157	817	1593	95	below_threshold
Rhodococcus jostii	strain=NBRC 16295	GCA_001894825.1	132919	132919	type	True	79.7756	793	1593	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:07,378] [INFO] DFAST Taxonomy check result was written to GCF_006704125.1_ASM670412v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:07,379] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:07,379] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:07,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/checkm_data
[2024-01-24 12:30:07,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:07,427] [INFO] Task started: CheckM
[2024-01-24 12:30:07,427] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006704125.1_ASM670412v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006704125.1_ASM670412v1_genomic.fna/checkm_input GCF_006704125.1_ASM670412v1_genomic.fna/checkm_result
[2024-01-24 12:31:01,190] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:01,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:01,218] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:01,218] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:01,219] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006704125.1_ASM670412v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:01,219] [INFO] Task started: Blastn
[2024-01-24 12:31:01,219] [INFO] Running command: blastn -query GCF_006704125.1_ASM670412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga42ad751-08ba-40a6-bea0-d8321e2ae6bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_006704125.1_ASM670412v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:03,099] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:03,103] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:03,103] [INFO] Target genome list was writen to GCF_006704125.1_ASM670412v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:03,113] [INFO] Task started: fastANI
[2024-01-24 12:31:03,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg7625892d-bd4a-44a1-b868-14a01e717bee/GCF_006704125.1_ASM670412v1_genomic.fna.gz --refList GCF_006704125.1_ASM670412v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006704125.1_ASM670412v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:18,460] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:18,474] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:18,475] [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_006704125.1	s__Rhodococcus sp006704125	100.0	1591	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001894985.1	s__Rhodococcus tukisamuensis	83.5497	1150	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_005049235.1	s__Rhodococcus oryzae	83.1003	1107	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_001894865.1	s__Rhodococcus maanshanensis	83.0727	1123	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_001040705.1	s__Rhodococcus sp001040705	81.8459	1011	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.99	95.99	0.87	0.87	2	-
GCF_000341795.1	s__Rhodococcus triatomae_A	81.5882	1008	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434945.1	s__Rhodococcus subtropicus	80.9115	771	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	80.9089	905	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738775.1	s__Rhodococcus defluvii	80.7958	819	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005484805.1	s__Rhodococcus sp005484805	80.6231	841	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894825.1	s__Rhodococcus jostii	79.7586	796	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	79.6483	841	1593	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:18,478] [INFO] GTDB search result was written to GCF_006704125.1_ASM670412v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:18,479] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:18,487] [INFO] DFAST_QC result json was written to GCF_006704125.1_ASM670412v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:18,487] [INFO] DFAST_QC completed!
[2024-01-24 12:31:18,487] [INFO] Total running time: 0h1m49s