[2024-01-24 13:31:31,190] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:31,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:31,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference
[2024-01-24 13:31:32,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:32,455] [INFO] Task started: Prodigal
[2024-01-24 13:31:32,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg13d81d92-e61b-49d0-b0cd-4f22dacfa143/GCF_001894985.1_ASM189498v1_genomic.fna.gz | prodigal -d GCF_001894985.1_ASM189498v1_genomic.fna/cds.fna -a GCF_001894985.1_ASM189498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:58,387] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:58,388] [INFO] Task started: HMMsearch
[2024-01-24 13:31:58,388] [INFO] Running command: hmmsearch --tblout GCF_001894985.1_ASM189498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/reference_markers.hmm GCF_001894985.1_ASM189498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:58,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:58,806] [INFO] Found 6/6 markers.
[2024-01-24 13:31:58,867] [INFO] Query marker FASTA was written to GCF_001894985.1_ASM189498v1_genomic.fna/markers.fasta
[2024-01-24 13:31:58,867] [INFO] Task started: Blastn
[2024-01-24 13:31:58,867] [INFO] Running command: blastn -query GCF_001894985.1_ASM189498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/reference_markers.fasta -out GCF_001894985.1_ASM189498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:00,304] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:00,308] [INFO] Selected 7 target genomes.
[2024-01-24 13:32:00,309] [INFO] Target genome list was writen to GCF_001894985.1_ASM189498v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:00,316] [INFO] Task started: fastANI
[2024-01-24 13:32:00,316] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d81d92-e61b-49d0-b0cd-4f22dacfa143/GCF_001894985.1_ASM189498v1_genomic.fna.gz --refList GCF_001894985.1_ASM189498v1_genomic.fna/target_genomes.txt --output GCF_001894985.1_ASM189498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:10,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:10,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:10,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:10,323] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:10,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:10,323] [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 tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	100.0	1796	1801	95	conclusive
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	99.9928	1791	1801	95	conclusive
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	83.6585	1192	1801	95	below_threshold
Rhodococcus spelaei	strain=C9-5	GCA_006704125.1	2546320	2546320	type	True	83.5434	1139	1801	95	below_threshold
Rhodococcus maanshanensis	strain=NBRC 100610	GCA_001894865.1	183556	183556	type	True	83.4275	1162	1801	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	83.389	1173	1801	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	81.0604	895	1801	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:10,327] [INFO] DFAST Taxonomy check result was written to GCF_001894985.1_ASM189498v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:10,328] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:10,328] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:10,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/checkm_data
[2024-01-24 13:32:10,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:10,392] [INFO] Task started: CheckM
[2024-01-24 13:32:10,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001894985.1_ASM189498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001894985.1_ASM189498v1_genomic.fna/checkm_input GCF_001894985.1_ASM189498v1_genomic.fna/checkm_result
[2024-01-24 13:33:24,781] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:24,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:24,808] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:24,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:24,809] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001894985.1_ASM189498v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:24,809] [INFO] Task started: Blastn
[2024-01-24 13:33:24,810] [INFO] Running command: blastn -query GCF_001894985.1_ASM189498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg91e2d419-04c5-4765-bd12-b3bddef6bd66/dqc_reference/reference_markers_gtdb.fasta -out GCF_001894985.1_ASM189498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:26,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:26,917] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:26,917] [INFO] Target genome list was writen to GCF_001894985.1_ASM189498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:26,927] [INFO] Task started: fastANI
[2024-01-24 13:33:26,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg13d81d92-e61b-49d0-b0cd-4f22dacfa143/GCF_001894985.1_ASM189498v1_genomic.fna.gz --refList GCF_001894985.1_ASM189498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001894985.1_ASM189498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:43,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:43,131] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:43,132] [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_001894985.1	s__Rhodococcus tukisamuensis	100.0	1796	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_005049235.1	s__Rhodococcus oryzae	83.6697	1190	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	95.56	95.24	0.93	0.92	5	-
GCF_006704125.1	s__Rhodococcus sp006704125	83.5353	1140	1801	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	83.4111	1166	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_013348805.1	s__Rhodococcus sp003350365	81.3152	977	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_004011865.1	s__Rhodococcus agglutinans	81.2984	976	1801	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	81.063	896	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001646645.1	s__Rhodococcus hoagii	80.9304	795	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_005484805.1	s__Rhodococcus sp005484805	80.666	857	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068395.1	s__Rhodococcus sp002165735	80.0931	911	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_012396235.1	s__Rhodococcus opacus	79.8816	871	1801	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:43,133] [INFO] GTDB search result was written to GCF_001894985.1_ASM189498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:43,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:43,136] [INFO] DFAST_QC result json was written to GCF_001894985.1_ASM189498v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:43,137] [INFO] DFAST_QC completed!
[2024-01-24 13:33:43,137] [INFO] Total running time: 0h2m12s