[2024-01-24 13:55:18,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference
[2024-01-24 13:55:20,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:20,021] [INFO] Task started: Prodigal
[2024-01-24 13:55:20,022] [INFO] Running command: gunzip -c /var/lib/cwl/stg54c5c5b2-1bc0-41d1-91b9-cec61bc2e14a/GCF_009176285.1_ASM917628v1_genomic.fna.gz | prodigal -d GCF_009176285.1_ASM917628v1_genomic.fna/cds.fna -a GCF_009176285.1_ASM917628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:41,004] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:41,005] [INFO] Task started: HMMsearch
[2024-01-24 13:55:41,005] [INFO] Running command: hmmsearch --tblout GCF_009176285.1_ASM917628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/reference_markers.hmm GCF_009176285.1_ASM917628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:41,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:41,423] [INFO] Found 6/6 markers.
[2024-01-24 13:55:41,482] [INFO] Query marker FASTA was written to GCF_009176285.1_ASM917628v1_genomic.fna/markers.fasta
[2024-01-24 13:55:41,483] [INFO] Task started: Blastn
[2024-01-24 13:55:41,483] [INFO] Running command: blastn -query GCF_009176285.1_ASM917628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/reference_markers.fasta -out GCF_009176285.1_ASM917628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:42,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:42,895] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:42,895] [INFO] Target genome list was writen to GCF_009176285.1_ASM917628v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:42,919] [INFO] Task started: fastANI
[2024-01-24 13:55:42,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c5c5b2-1bc0-41d1-91b9-cec61bc2e14a/GCF_009176285.1_ASM917628v1_genomic.fna.gz --refList GCF_009176285.1_ASM917628v1_genomic.fna/target_genomes.txt --output GCF_009176285.1_ASM917628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:59,222] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:59,222] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:59,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:59,232] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:55:59,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:59,232] [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 aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	100.0	2062	2069	95	conclusive
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	99.9524	1995	2069	95	conclusive
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	91.9853	1529	2069	95	below_threshold
Rhodococcus ruber	strain=DSM 43338	GCA_001646835.1	1830	1830	type	True	91.8703	1476	2069	95	below_threshold
Rhodococcus zopfii	strain=NBRC 100606	GCA_001895025.1	43772	43772	type	True	82.3733	1149	2069	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	81.8567	1070	2069	95	below_threshold
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	81.383	941	2069	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	80.5574	853	2069	95	below_threshold
Prescottella subtropica	strain=C9-28	GCA_005434945.1	2545757	2545757	type	True	80.348	777	2069	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	80.2052	797	2069	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:59,234] [INFO] DFAST Taxonomy check result was written to GCF_009176285.1_ASM917628v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:59,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:59,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:59,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/checkm_data
[2024-01-24 13:55:59,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:59,298] [INFO] Task started: CheckM
[2024-01-24 13:55:59,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009176285.1_ASM917628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009176285.1_ASM917628v1_genomic.fna/checkm_input GCF_009176285.1_ASM917628v1_genomic.fna/checkm_result
[2024-01-24 13:57:11,268] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:11,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:11,296] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:11,296] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:11,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009176285.1_ASM917628v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:11,297] [INFO] Task started: Blastn
[2024-01-24 13:57:11,297] [INFO] Running command: blastn -query GCF_009176285.1_ASM917628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c554a9d-7ba4-47d3-9918-4abaff594883/dqc_reference/reference_markers_gtdb.fasta -out GCF_009176285.1_ASM917628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:13,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:13,372] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:13,373] [INFO] Target genome list was writen to GCF_009176285.1_ASM917628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:13,394] [INFO] Task started: fastANI
[2024-01-24 13:57:13,395] [INFO] Running command: fastANI --query /var/lib/cwl/stg54c5c5b2-1bc0-41d1-91b9-cec61bc2e14a/GCF_009176285.1_ASM917628v1_genomic.fna.gz --refList GCF_009176285.1_ASM917628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009176285.1_ASM917628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:29,350] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:29,361] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:29,361] [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_011058165.1	s__Rhodococcus aetherivorans	99.9524	1995	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	conclusive
GCF_001894945.1	s__Rhodococcus ruber	91.9738	1530	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	-
GCF_001895025.1	s__Rhodococcus zopfii	82.3624	1152	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.81	97.81	0.87	0.87	2	-
GCF_015865005.1	s__Rhodococcus sp015865005	82.1438	1101	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646785.1	s__Rhodococcus phenolicus	81.8624	1068	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105195.1	s__Rhodococcus pyridinivorans	81.4553	980	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.16	95.17	0.90	0.84	21	-
GCF_900187265.1	s__Rhodococcus rhodochrous	81.3591	958	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	-
GCF_001646655.1	s__Rhodococcus gordoniae	81.2983	914	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_004011865.1	s__Rhodococcus agglutinans	80.5314	857	2069	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	80.3541	775	2069	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	80.1654	802	2069	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:29,363] [INFO] GTDB search result was written to GCF_009176285.1_ASM917628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:29,363] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:29,367] [INFO] DFAST_QC result json was written to GCF_009176285.1_ASM917628v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:29,368] [INFO] DFAST_QC completed!
[2024-01-24 13:57:29,368] [INFO] Total running time: 0h2m11s