[2024-01-24 15:10:20,025] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:20,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:20,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference
[2024-01-24 15:10:22,719] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,720] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a01c522-3521-46ff-91f0-cf890a7aba74/GCF_016482825.1_ASM1648282v1_genomic.fna.gz | prodigal -d GCF_016482825.1_ASM1648282v1_genomic.fna/cds.fna -a GCF_016482825.1_ASM1648282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:48,415] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:48,415] [INFO] Task started: HMMsearch
[2024-01-24 15:10:48,415] [INFO] Running command: hmmsearch --tblout GCF_016482825.1_ASM1648282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/reference_markers.hmm GCF_016482825.1_ASM1648282v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:48,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:48,770] [INFO] Found 6/6 markers.
[2024-01-24 15:10:48,838] [INFO] Query marker FASTA was written to GCF_016482825.1_ASM1648282v1_genomic.fna/markers.fasta
[2024-01-24 15:10:48,839] [INFO] Task started: Blastn
[2024-01-24 15:10:48,839] [INFO] Running command: blastn -query GCF_016482825.1_ASM1648282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/reference_markers.fasta -out GCF_016482825.1_ASM1648282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:50,005] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:50,009] [INFO] Selected 24 target genomes.
[2024-01-24 15:10:50,009] [INFO] Target genome list was writen to GCF_016482825.1_ASM1648282v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:50,025] [INFO] Task started: fastANI
[2024-01-24 15:10:50,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a01c522-3521-46ff-91f0-cf890a7aba74/GCF_016482825.1_ASM1648282v1_genomic.fna.gz --refList GCF_016482825.1_ASM1648282v1_genomic.fna/target_genomes.txt --output GCF_016482825.1_ASM1648282v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:18,977] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:18,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:18,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:18,995] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:18,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:18,996] [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
Antrihabitans stalagmiti	strain=YC3-6	GCA_016482825.1	2799499	2799499	type	True	100.0	2107	2108	95	conclusive
Antrihabitans stalactiti	strain=YC2-7	GCA_012932915.1	2584121	2584121	type	True	79.0131	780	2108	95	below_threshold
Rhodococcus cavernicola	strain=C1-24	GCA_008297975.1	2495913	2495913	type	True	78.4665	620	2108	95	below_threshold
Rhodococcus oryzae	strain=NEAU-CX67	GCA_005049235.1	2571143	2571143	type	True	78.1051	500	2108	95	below_threshold
Prescottella agglutinans	strain=CCTCC AB2014297	GCA_004011865.1	1644129	1644129	type	True	78.0976	500	2108	95	below_threshold
Rhodococcus tukisamuensis	strain=JCM 11308	GCA_900101735.1	168276	168276	type	True	78.0668	466	2108	95	below_threshold
Rhodococcus tukisamuensis	strain=NBRC 100609	GCA_001894985.1	168276	168276	type	True	78.0465	467	2108	95	below_threshold
Aldersonia kunmingensis	strain=DSM 45001	GCA_001646865.1	408066	408066	type	True	77.9829	471	2108	95	below_threshold
Rhodococcus rhodnii	strain=ATCC 35071	GCA_008011915.1	38312	38312	type	True	77.9206	401	2108	95	below_threshold
Rhodococcus rhodnii	strain=NBRC 100604	GCA_001894925.1	38312	38312	type	True	77.892	397	2108	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	77.8616	540	2108	95	below_threshold
Nocardia rosealba	strain=NEAU-G4	GCA_020216065.1	2878563	2878563	type	True	77.8396	470	2108	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	77.8279	588	2108	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	77.7981	528	2108	95	below_threshold
Nocardia xishanensis	strain=NBRC 101358	GCA_001613365.1	238964	238964	type	True	77.6228	536	2108	95	below_threshold
Rhodococcus marinonascens	strain=NBRC 14363	GCA_001894885.1	38311	38311	type	True	77.6026	330	2108	95	below_threshold
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	77.6009	532	2108	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	77.5883	480	2108	95	below_threshold
Nocardia pseudovaccinii	strain=NBRC 100343	GCA_001613225.1	189540	189540	type	True	77.5196	437	2108	95	below_threshold
Nocardia mexicana	strain=NBRC 108244	GCA_001613165.1	279262	279262	type	True	77.0008	510	2108	95	below_threshold
Cupriavidus respiraculi	strain=LMG 21510	GCA_914271545.1	195930	195930	type	True	75.1085	65	2108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:18,999] [INFO] DFAST Taxonomy check result was written to GCF_016482825.1_ASM1648282v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:19,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:19,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:19,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/checkm_data
[2024-01-24 15:11:19,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:19,065] [INFO] Task started: CheckM
[2024-01-24 15:11:19,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016482825.1_ASM1648282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016482825.1_ASM1648282v1_genomic.fna/checkm_input GCF_016482825.1_ASM1648282v1_genomic.fna/checkm_result
[2024-01-24 15:12:31,332] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:31,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:31,367] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:31,367] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:31,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016482825.1_ASM1648282v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:31,368] [INFO] Task started: Blastn
[2024-01-24 15:12:31,369] [INFO] Running command: blastn -query GCF_016482825.1_ASM1648282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3fd91bcf-a685-420c-a289-93692b2b0033/dqc_reference/reference_markers_gtdb.fasta -out GCF_016482825.1_ASM1648282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:32,923] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:32,927] [INFO] Selected 23 target genomes.
[2024-01-24 15:12:32,927] [INFO] Target genome list was writen to GCF_016482825.1_ASM1648282v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:32,943] [INFO] Task started: fastANI
[2024-01-24 15:12:32,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a01c522-3521-46ff-91f0-cf890a7aba74/GCF_016482825.1_ASM1648282v1_genomic.fna.gz --refList GCF_016482825.1_ASM1648282v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016482825.1_ASM1648282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:01,730] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:01,751] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:01,751] [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_016482825.1	s__Antrihabitans sp016482825	100.0	2107	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Antrihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016481275.1	s__Antrihabitans sp016481275	79.5391	827	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Antrihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932915.1	s__Antrihabitans stalactiti	78.996	783	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Antrihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008297975.1	s__C1-24 sp008297975	78.4847	619	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__C1-24	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011865.1	s__Rhodococcus agglutinans	78.0763	503	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894985.1	s__Rhodococcus tukisamuensis	78.0402	467	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001426185.1	s__Rhodococcus_C sp001426185	77.9886	368	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	99.01	98.03	0.95	0.90	3	-
GCF_001646865.1	s__Aldersonia kunmingensis	77.9809	472	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Aldersonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341795.1	s__Rhodococcus triatomae_A	77.8279	461	2108	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	77.8035	593	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_019222765.1	s__Nocardia iowensis	77.7984	528	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	77.7884	504	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
GCF_010868145.1	s__Nocardia cyriacigeorgica_D	77.6643	439	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.70	99.66	0.98	0.98	4	-
GCF_001613365.1	s__Nocardia xishanensis	77.6099	538	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894885.1	s__Rhodococcus marinonascens	77.5933	331	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130705.1	s__Rhodococcus sp003130705	77.5874	480	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.82	95.95	0.80	0.77	4	-
GCF_001613225.1	s__Nocardia pseudovaccinii	77.5142	436	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	77.4789	503	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858475.1	s__Tsukamurella conjunctivitidis	77.3447	292	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	-
GCF_001613165.1	s__Nocardia mexicana	76.9991	511	2108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:01,753] [INFO] GTDB search result was written to GCF_016482825.1_ASM1648282v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:01,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:01,758] [INFO] DFAST_QC result json was written to GCF_016482825.1_ASM1648282v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:01,758] [INFO] DFAST_QC completed!
[2024-01-24 15:13:01,758] [INFO] Total running time: 0h2m42s