[2024-01-24 11:44:22,867] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:22,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:22,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe2290ee-ab97-4247-9884-08ce198f33c6/GCF_003130705.1_ASM313070v1_genomic.fna.gz | prodigal -d GCF_003130705.1_ASM313070v1_genomic.fna/cds.fna -a GCF_003130705.1_ASM313070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:11,699] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:11,699] [INFO] Task started: HMMsearch
[2024-01-24 11:45:11,699] [INFO] Running command: hmmsearch --tblout GCF_003130705.1_ASM313070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/reference_markers.hmm GCF_003130705.1_ASM313070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:12,030] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:12,031] [INFO] Found 6/6 markers.
[2024-01-24 11:45:12,094] [INFO] Query marker FASTA was written to GCF_003130705.1_ASM313070v1_genomic.fna/markers.fasta
[2024-01-24 11:45:12,095] [INFO] Task started: Blastn
[2024-01-24 11:45:12,095] [INFO] Running command: blastn -query GCF_003130705.1_ASM313070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/reference_markers.fasta -out GCF_003130705.1_ASM313070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:13,221] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:13,224] [INFO] Selected 12 target genomes.
[2024-01-24 11:45:13,225] [INFO] Target genome list was writen to GCF_003130705.1_ASM313070v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:13,230] [INFO] Task started: fastANI
[2024-01-24 11:45:13,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe2290ee-ab97-4247-9884-08ce198f33c6/GCF_003130705.1_ASM313070v1_genomic.fna.gz --refList GCF_003130705.1_ASM313070v1_genomic.fna/target_genomes.txt --output GCF_003130705.1_ASM313070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:33,532] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:33,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:33,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:33,546] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:33,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:33,546] [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 oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	100.0	2668	2669	95	conclusive
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	84.3218	1529	2669	95	below_threshold
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	84.0937	1544	2669	95	below_threshold
Rhodococcus koreensis	strain=NBRC 100607	GCA_001894845.1	99653	99653	type	True	84.0284	1657	2669	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	83.9134	1634	2669	95	below_threshold
Rhodococcus wratislaviensis	strain=NCTC13229	GCA_900455735.1	44752	44752	suspected-type	True	83.8795	1464	2669	95	below_threshold
Rhodococcus wratislaviensis	strain=NBRC 100605	GCA_000583735.1	44752	44752	suspected-type	True	83.8425	1608	2669	95	below_threshold
Rhodococcus jostii	strain=DSM 44719	GCA_900105375.1	132919	132919	type	True	83.6793	1600	2669	95	below_threshold
Rhodococcus qingshengii	strain=djl-6	GCA_023221595.1	334542	334542	type	True	79.0164	656	2669	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	78.9246	714	2669	95	below_threshold
Rhodococcus erythropolis	strain=JCM 3201	GCA_003990875.1	1833	1833	type	True	78.8486	650	2669	95	below_threshold
Rhodococcus erythropolis	strain=DSM 43066	GCA_022134675.1	1833	1833	type	True	78.7252	651	2669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:33,548] [INFO] DFAST Taxonomy check result was written to GCF_003130705.1_ASM313070v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:33,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:33,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:33,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/checkm_data
[2024-01-24 11:45:33,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:33,630] [INFO] Task started: CheckM
[2024-01-24 11:45:33,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003130705.1_ASM313070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003130705.1_ASM313070v1_genomic.fna/checkm_input GCF_003130705.1_ASM313070v1_genomic.fna/checkm_result
[2024-01-24 11:47:34,790] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:34,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:34,818] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:34,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:34,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003130705.1_ASM313070v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:34,819] [INFO] Task started: Blastn
[2024-01-24 11:47:34,820] [INFO] Running command: blastn -query GCF_003130705.1_ASM313070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58915c94-66cd-46d0-895e-a310b98e2cfa/dqc_reference/reference_markers_gtdb.fasta -out GCF_003130705.1_ASM313070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:36,415] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:36,419] [INFO] Selected 11 target genomes.
[2024-01-24 11:47:36,419] [INFO] Target genome list was writen to GCF_003130705.1_ASM313070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:36,428] [INFO] Task started: fastANI
[2024-01-24 11:47:36,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe2290ee-ab97-4247-9884-08ce198f33c6/GCF_003130705.1_ASM313070v1_genomic.fna.gz --refList GCF_003130705.1_ASM313070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003130705.1_ASM313070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:56,994] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:57,011] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:57,011] [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_003130705.1	s__Rhodococcus sp003130705	100.0	2668	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.82	95.95	0.80	0.77	4	conclusive
GCF_000014565.1	s__Rhodococcus jostii_A	84.594	1681	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_900105905.1	s__Rhodococcus koreensis	84.0939	1697	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.00	98.46	0.87	0.80	4	-
GCF_012396235.1	s__Rhodococcus opacus	84.089	1546	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
GCF_017068395.1	s__Rhodococcus sp002165735	83.9066	1637	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	83.8633	1469	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
GCF_000010805.1	s__Rhodococcus opacus_C	83.8042	1602	2669	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	83.5871	1574	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014256275.1	s__Rhodococcus wratislaviensis_A	83.4362	1606	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.9073	716	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552595.1	s__Rhodococcus erythropolis	78.7602	640	2669	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.5281	98.72	98.39	0.92	0.80	38	-
--------------------------------------------------------------------------------
[2024-01-24 11:47:57,013] [INFO] GTDB search result was written to GCF_003130705.1_ASM313070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:57,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:57,017] [INFO] DFAST_QC result json was written to GCF_003130705.1_ASM313070v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:57,017] [INFO] DFAST_QC completed!
[2024-01-24 11:47:57,018] [INFO] Total running time: 0h3m34s