[2024-01-24 12:07:06,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference
[2024-01-24 12:07:07,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,917] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg27e26065-458e-46bc-a5c7-0d6b82d9dec8/GCF_016599245.1_ASM1659924v1_genomic.fna.gz | prodigal -d GCF_016599245.1_ASM1659924v1_genomic.fna/cds.fna -a GCF_016599245.1_ASM1659924v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:22,141] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:22,141] [INFO] Task started: HMMsearch
[2024-01-24 12:07:22,142] [INFO] Running command: hmmsearch --tblout GCF_016599245.1_ASM1659924v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/reference_markers.hmm GCF_016599245.1_ASM1659924v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:22,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:22,478] [INFO] Found 6/6 markers.
[2024-01-24 12:07:22,524] [INFO] Query marker FASTA was written to GCF_016599245.1_ASM1659924v1_genomic.fna/markers.fasta
[2024-01-24 12:07:22,524] [INFO] Task started: Blastn
[2024-01-24 12:07:22,524] [INFO] Running command: blastn -query GCF_016599245.1_ASM1659924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/reference_markers.fasta -out GCF_016599245.1_ASM1659924v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:23,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:23,782] [INFO] Selected 19 target genomes.
[2024-01-24 12:07:23,782] [INFO] Target genome list was writen to GCF_016599245.1_ASM1659924v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:23,787] [INFO] Task started: fastANI
[2024-01-24 12:07:23,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg27e26065-458e-46bc-a5c7-0d6b82d9dec8/GCF_016599245.1_ASM1659924v1_genomic.fna.gz --refList GCF_016599245.1_ASM1659924v1_genomic.fna/target_genomes.txt --output GCF_016599245.1_ASM1659924v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:41,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:41,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:41,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:41,754] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:41,754] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:41,754] [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
Tomitella biformata	strain=DSM 45403	GCA_016599245.1	630403	630403	type	True	100.0	1541	1544	95	conclusive
Tomitella biformata	strain=AHU 1821	GCA_000524475.1	630403	630403	type	True	99.993	1515	1544	95	conclusive
Tomitella fengzijianii	strain=HY188	GCA_007559025.1	2597660	2597660	type	True	79.3551	577	1544	95	below_threshold
Tomitella fengzijianii	strain=HY188	GCA_023162105.1	2597660	2597660	type	True	79.3066	581	1544	95	below_threshold
Tomitella gaofuii	strain=HY172	GCA_014126825.1	2760083	2760083	type	True	79.0765	614	1544	95	below_threshold
Tomitella gaofuii	strain=HY172	GCA_023162085.1	2760083	2760083	type	True	79.0447	609	1544	95	below_threshold
Tomitella cavernea	strain=JCM 18542	GCA_016599145.1	1387982	1387982	type	True	78.8611	574	1544	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	78.7245	531	1544	95	below_threshold
Rhodococcus aetherivorans	strain=DSM 44752	GCA_011058165.1	191292	191292	type	True	78.4081	535	1544	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	78.3625	500	1544	95	below_threshold
Rhodococcus aetherivorans	strain=JCM 14343	GCA_009176285.1	191292	191292	type	True	78.2845	536	1544	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	78.2771	500	1544	95	below_threshold
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	78.2402	534	1544	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	78.0687	496	1544	95	below_threshold
Nocardia farcinica	strain=NBRC 15532	GCA_001612925.1	37329	37329	type	True	78.0536	489	1544	95	below_threshold
Nocardia farcinica	strain=NCTC11134	GCA_001182745.2	37329	37329	type	True	78.0144	507	1544	95	below_threshold
Nocardia puris	strain=DSM 44599	GCA_003315035.1	208602	208602	type	True	77.8844	493	1544	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	77.7594	459	1544	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	77.497	477	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:41,757] [INFO] DFAST Taxonomy check result was written to GCF_016599245.1_ASM1659924v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:41,758] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:41,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:41,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/checkm_data
[2024-01-24 12:07:41,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:41,809] [INFO] Task started: CheckM
[2024-01-24 12:07:41,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016599245.1_ASM1659924v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016599245.1_ASM1659924v1_genomic.fna/checkm_input GCF_016599245.1_ASM1659924v1_genomic.fna/checkm_result
[2024-01-24 12:08:23,905] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:23,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:23,927] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:23,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:23,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016599245.1_ASM1659924v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:23,929] [INFO] Task started: Blastn
[2024-01-24 12:08:23,929] [INFO] Running command: blastn -query GCF_016599245.1_ASM1659924v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44f0e81d-9f2a-4b93-8ce0-0e84e1d9e809/dqc_reference/reference_markers_gtdb.fasta -out GCF_016599245.1_ASM1659924v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:25,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:25,792] [INFO] Selected 20 target genomes.
[2024-01-24 12:08:25,792] [INFO] Target genome list was writen to GCF_016599245.1_ASM1659924v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:25,801] [INFO] Task started: fastANI
[2024-01-24 12:08:25,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg27e26065-458e-46bc-a5c7-0d6b82d9dec8/GCF_016599245.1_ASM1659924v1_genomic.fna.gz --refList GCF_016599245.1_ASM1659924v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016599245.1_ASM1659924v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:46,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:46,621] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:46,621] [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_000524475.1	s__Tomitella biformata	99.993	1515	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007559025.1	s__Tomitella sp007559025	79.355	577	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	99.43	99.43	0.96	0.96	2	-
GCF_014126825.1	s__Tomitella sp014126825	79.0608	616	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	97.57	97.57	0.88	0.88	2	-
GCF_016599145.1	s__Tomitella cavernea	78.8411	576	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tomitella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894865.1	s__Rhodococcus maanshanensis	78.7517	528	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.18	96.37	0.94	0.89	3	-
GCF_006704125.1	s__Rhodococcus sp006704125	78.745	523	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013348805.1	s__Rhodococcus sp003350365	78.5107	512	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.85	98.85	0.92	0.92	2	-
GCF_001646645.1	s__Rhodococcus hoagii	78.4652	472	1544	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	78.4134	488	1544	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	78.4053	534	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.92	95.74	0.88	0.78	18	-
GCF_001894945.1	s__Rhodococcus ruber	78.2622	531	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	-
GCF_001182745.1	s__Nocardia farcinica	78.0372	503	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_003315035.1	s__Nocardia puris	77.9202	486	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.66	99.46	0.95	0.92	4	-
GCF_000014565.1	s__Rhodococcus jostii_A	77.8851	494	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	97.76	95.96	0.81	0.77	4	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	77.8061	480	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477835.1	s__Nocardia higoensis_A	77.7894	418	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308715.1	s__Nocardia tenerifensis	77.7818	456	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010858045.1	s__Nocardia cyriacigeorgica_E	77.7574	397	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.94	98.91	0.92	0.91	4	-
GCF_015477355.1	s__Nocardia blacklockiae	77.5226	490	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612885.1	s__Nocardia harenae	77.4779	480	1544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:46,623] [INFO] GTDB search result was written to GCF_016599245.1_ASM1659924v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:46,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:46,628] [INFO] DFAST_QC result json was written to GCF_016599245.1_ASM1659924v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:46,628] [INFO] DFAST_QC completed!
[2024-01-24 12:08:46,628] [INFO] Total running time: 0h1m40s