[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,127] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,128] [INFO] DQC Reference Directory: /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference
[2024-01-25 17:34:08,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,951] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg47f91c81-c519-47ed-9c56-9d0af2669e8e/GCF_001895045.1_ASM189504v1_genomic.fna.gz | prodigal -d GCF_001895045.1_ASM189504v1_genomic.fna/cds.fna -a GCF_001895045.1_ASM189504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:23,463] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:23,464] [INFO] Task started: HMMsearch
[2024-01-25 17:34:23,464] [INFO] Running command: hmmsearch --tblout GCF_001895045.1_ASM189504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/reference_markers.hmm GCF_001895045.1_ASM189504v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:23,742] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:23,743] [INFO] Found 6/6 markers.
[2024-01-25 17:34:23,788] [INFO] Query marker FASTA was written to GCF_001895045.1_ASM189504v1_genomic.fna/markers.fasta
[2024-01-25 17:34:23,788] [INFO] Task started: Blastn
[2024-01-25 17:34:23,789] [INFO] Running command: blastn -query GCF_001895045.1_ASM189504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/reference_markers.fasta -out GCF_001895045.1_ASM189504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:24,905] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:24,908] [INFO] Selected 13 target genomes.
[2024-01-25 17:34:24,909] [INFO] Target genome list was writen to GCF_001895045.1_ASM189504v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:24,913] [INFO] Task started: fastANI
[2024-01-25 17:34:24,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f91c81-c519-47ed-9c56-9d0af2669e8e/GCF_001895045.1_ASM189504v1_genomic.fna.gz --refList GCF_001895045.1_ASM189504v1_genomic.fna/target_genomes.txt --output GCF_001895045.1_ASM189504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:39,235] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:39,236] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:39,236] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:39,245] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:34:39,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:39,245] [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 coprophilus	strain=NBRC 100603	GCA_001895045.1	38310	38310	type	True	100.0	1501	1502	95	conclusive
Rhodococcus coprophilus	strain=NCTC10994	GCA_900478115.1	38310	38310	type	True	99.9999	1501	1502	95	conclusive
Rhodococcus rhodochrous	strain=DSM 43241	GCA_001646825.1	1829	1829	suspected-type	True	81.5379	935	1502	95	below_threshold
Rhodococcus rhodochrous	strain=NBRC 16069	GCA_001047055.1	1829	1829	suspected-type	True	81.5045	950	1502	95	below_threshold
Rhodococcus rhodochrous	strain=NCTC10210	GCA_900187265.1	1829	1829	suspected-type	True	81.4808	970	1502	95	below_threshold
Rhodococcus pyridinivorans	strain=DSM 44555	GCA_900105195.1	103816	103816	type	True	81.3471	909	1502	95	below_threshold
Rhodococcus pyridinivorans	strain=DSM 44555	GCA_001646805.1	103816	103816	type	True	81.3221	882	1502	95	below_threshold
Rhodococcus pyridinivorans	strain=NBRC 100608	GCA_001894905.1	103816	103816	type	True	81.302	918	1502	95	below_threshold
Rhodococcus zopfii	strain=NBRC 100606	GCA_001895025.1	43772	43772	type	True	80.708	822	1502	95	below_threshold
Rhodococcus phenolicus	strain=DSM 44812	GCA_001646785.1	263849	263849	type	True	80.6618	846	1502	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	80.2334	798	1502	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	80.2185	809	1502	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	79.3689	611	1502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:39,246] [INFO] DFAST Taxonomy check result was written to GCF_001895045.1_ASM189504v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:39,247] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:39,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:39,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/checkm_data
[2024-01-25 17:34:39,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:39,297] [INFO] Task started: CheckM
[2024-01-25 17:34:39,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001895045.1_ASM189504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001895045.1_ASM189504v1_genomic.fna/checkm_input GCF_001895045.1_ASM189504v1_genomic.fna/checkm_result
[2024-01-25 17:35:27,598] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:27,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:27,622] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:27,623] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:27,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001895045.1_ASM189504v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:27,623] [INFO] Task started: Blastn
[2024-01-25 17:35:27,624] [INFO] Running command: blastn -query GCF_001895045.1_ASM189504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg379e1dfd-9119-4206-a0f2-a29ca25eea02/dqc_reference/reference_markers_gtdb.fasta -out GCF_001895045.1_ASM189504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:29,322] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:29,324] [INFO] Selected 13 target genomes.
[2024-01-25 17:35:29,325] [INFO] Target genome list was writen to GCF_001895045.1_ASM189504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:29,333] [INFO] Task started: fastANI
[2024-01-25 17:35:29,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f91c81-c519-47ed-9c56-9d0af2669e8e/GCF_001895045.1_ASM189504v1_genomic.fna.gz --refList GCF_001895045.1_ASM189504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001895045.1_ASM189504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:45,365] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:45,374] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:45,375] [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_001895045.1	s__Rhodococcus coprophilus	100.0	1501	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_012844225.1	s__Rhodococcus sp012844225	87.7361	1257	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.09	99.02	0.95	0.95	3	-
GCF_900187265.1	s__Rhodococcus rhodochrous	81.4615	972	1502	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	81.3648	863	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.98	98.16	0.95	0.93	4	-
GCF_900105195.1	s__Rhodococcus pyridinivorans	81.332	911	1502	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	81.2873	971	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015865005.1	s__Rhodococcus sp015865005	80.8206	847	1502	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	80.6998	662	1502	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	80.6713	846	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058165.1	s__Rhodococcus aetherivorans	80.2481	796	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_004345605.1	s__Rhodococcus sp004345605	80.1979	828	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012726195.1	s__Rhodococcus sp012726195	80.0901	792	1502	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	79.3884	608	1502	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:45,376] [INFO] GTDB search result was written to GCF_001895045.1_ASM189504v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:45,376] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:45,380] [INFO] DFAST_QC result json was written to GCF_001895045.1_ASM189504v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:45,380] [INFO] DFAST_QC completed!
[2024-01-25 17:35:45,380] [INFO] Total running time: 0h1m38s