[2024-01-24 14:13:18,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,451] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference
[2024-01-24 14:13:19,879] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:19,880] [INFO] Task started: Prodigal
[2024-01-24 14:13:19,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg33c5de4b-6e1a-4202-8935-7b0ff9845896/GCF_001047055.1_ASM104705v1_genomic.fna.gz | prodigal -d GCF_001047055.1_ASM104705v1_genomic.fna/cds.fna -a GCF_001047055.1_ASM104705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:39,378] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:39,378] [INFO] Task started: HMMsearch
[2024-01-24 14:13:39,378] [INFO] Running command: hmmsearch --tblout GCF_001047055.1_ASM104705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/reference_markers.hmm GCF_001047055.1_ASM104705v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:39,669] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:39,671] [INFO] Found 6/6 markers.
[2024-01-24 14:13:39,717] [INFO] Query marker FASTA was written to GCF_001047055.1_ASM104705v1_genomic.fna/markers.fasta
[2024-01-24 14:13:39,718] [INFO] Task started: Blastn
[2024-01-24 14:13:39,718] [INFO] Running command: blastn -query GCF_001047055.1_ASM104705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/reference_markers.fasta -out GCF_001047055.1_ASM104705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:40,979] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:40,983] [INFO] Selected 5 target genomes.
[2024-01-24 14:13:40,984] [INFO] Target genome list was writen to GCF_001047055.1_ASM104705v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:40,991] [INFO] Task started: fastANI
[2024-01-24 14:13:40,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c5de4b-6e1a-4202-8935-7b0ff9845896/GCF_001047055.1_ASM104705v1_genomic.fna.gz --refList GCF_001047055.1_ASM104705v1_genomic.fna/target_genomes.txt --output GCF_001047055.1_ASM104705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:47,713] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:47,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:47,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:47,722] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:13:47,723] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:47,723] [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 rhodochrous	strain=NBRC 16069	GCA_001047055.1	1829	1829	suspected-type	True	100.0	1693	1695	95	conclusive
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	99.999	1694	1695	95	conclusive
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	99.9899	1656	1695	95	conclusive
Rhodococcus pyridinivorans	strain=DSM 44555	GCA_900105195.1	103816	103816	type	True	94.8304	1416	1695	95	below_threshold
Rhodococcus pyridinivorans	strain=DSM 44555	GCA_001646805.1	103816	103816	type	True	94.753	1340	1695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:47,724] [INFO] DFAST Taxonomy check result was written to GCF_001047055.1_ASM104705v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:47,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:47,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:47,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/checkm_data
[2024-01-24 14:13:47,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:47,780] [INFO] Task started: CheckM
[2024-01-24 14:13:47,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001047055.1_ASM104705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001047055.1_ASM104705v1_genomic.fna/checkm_input GCF_001047055.1_ASM104705v1_genomic.fna/checkm_result
[2024-01-24 14:14:46,010] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:46,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:46,034] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:46,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:46,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001047055.1_ASM104705v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:46,036] [INFO] Task started: Blastn
[2024-01-24 14:14:46,036] [INFO] Running command: blastn -query GCF_001047055.1_ASM104705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa1dac17-c7dd-4fad-aa4c-e046afea9817/dqc_reference/reference_markers_gtdb.fasta -out GCF_001047055.1_ASM104705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:47,886] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:47,892] [INFO] Selected 8 target genomes.
[2024-01-24 14:14:47,893] [INFO] Target genome list was writen to GCF_001047055.1_ASM104705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:47,900] [INFO] Task started: fastANI
[2024-01-24 14:14:47,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg33c5de4b-6e1a-4202-8935-7b0ff9845896/GCF_001047055.1_ASM104705v1_genomic.fna.gz --refList GCF_001047055.1_ASM104705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001047055.1_ASM104705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:58,651] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:58,659] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:58,659] [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_900187265.1	s__Rhodococcus rhodochrous	99.999	1694	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.52	95.51	0.91	0.84	11	conclusive
GCF_900105195.1	s__Rhodococcus pyridinivorans	94.8304	1416	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.16	95.17	0.90	0.84	21	-
GCF_013602415.1	s__Rhodococcus sp013602415	91.0912	1477	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646655.1	s__Rhodococcus gordoniae	91.0816	1278	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_015865005.1	s__Rhodococcus sp015865005	82.1779	1019	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729135.1	s__Rhodococcus sp012729135	81.6894	784	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001895025.1	s__Rhodococcus zopfii	81.4282	1000	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.81	97.81	0.87	0.87	2	-
GCF_012844225.1	s__Rhodococcus sp012844225	81.3404	961	1695	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.09	99.02	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:58,661] [INFO] GTDB search result was written to GCF_001047055.1_ASM104705v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:58,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:58,664] [INFO] DFAST_QC result json was written to GCF_001047055.1_ASM104705v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:58,664] [INFO] DFAST_QC completed!
[2024-01-24 14:14:58,664] [INFO] Total running time: 0h1m40s