[2023-06-29 04:25:03,514] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:25:03,516] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:25:03,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference
[2023-06-29 04:25:05,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:25:05,417] [INFO] Task started: Prodigal
[2023-06-29 04:25:05,417] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c428ea4-e563-4489-ae80-e4042f0ac606/GCA_027592345.1_ASM2759234v1_genomic.fna.gz | prodigal -d GCA_027592345.1_ASM2759234v1_genomic.fna/cds.fna -a GCA_027592345.1_ASM2759234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:25:16,476] [INFO] Task succeeded: Prodigal
[2023-06-29 04:25:16,477] [INFO] Task started: HMMsearch
[2023-06-29 04:25:16,477] [INFO] Running command: hmmsearch --tblout GCA_027592345.1_ASM2759234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/reference_markers.hmm GCA_027592345.1_ASM2759234v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:25:16,768] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:25:16,769] [INFO] Found 6/6 markers.
[2023-06-29 04:25:16,805] [INFO] Query marker FASTA was written to GCA_027592345.1_ASM2759234v1_genomic.fna/markers.fasta
[2023-06-29 04:25:16,806] [INFO] Task started: Blastn
[2023-06-29 04:25:16,806] [INFO] Running command: blastn -query GCA_027592345.1_ASM2759234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/reference_markers.fasta -out GCA_027592345.1_ASM2759234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:25:17,939] [INFO] Task succeeded: Blastn
[2023-06-29 04:25:17,944] [INFO] Selected 32 target genomes.
[2023-06-29 04:25:17,945] [INFO] Target genome list was writen to GCA_027592345.1_ASM2759234v1_genomic.fna/target_genomes.txt
[2023-06-29 04:25:17,951] [INFO] Task started: fastANI
[2023-06-29 04:25:17,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c428ea4-e563-4489-ae80-e4042f0ac606/GCA_027592345.1_ASM2759234v1_genomic.fna.gz --refList GCA_027592345.1_ASM2759234v1_genomic.fna/target_genomes.txt --output GCA_027592345.1_ASM2759234v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:25:47,632] [INFO] Task succeeded: fastANI
[2023-06-29 04:25:47,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:25:47,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:25:47,656] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:25:47,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:25:47,656] [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
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.3567	574	1193	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.0012	662	1193	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	79.6367	534	1193	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.617	536	1193	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	79.5792	614	1193	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.497	621	1193	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	79.4826	566	1193	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.4633	618	1193	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	79.4264	573	1193	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	79.3589	635	1193	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	79.3036	620	1193	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	79.296	589	1193	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.1003	529	1193	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.0956	615	1193	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	79.0884	519	1193	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	79.0678	523	1193	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	79.0442	538	1193	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	78.9942	519	1193	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	78.8204	489	1193	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	78.7283	514	1193	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	78.6964	436	1193	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	78.6844	517	1193	95	below_threshold
Mycolicibacterium phocaicum	strain=JCM 15301	GCA_010731115.1	319706	319706	type	True	78.6124	475	1193	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	78.547	460	1193	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	78.4505	398	1193	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	78.4488	469	1193	95	below_threshold
Mycolicibacterium aubagnense	strain=DSM 45150	GCA_005670695.1	319707	319707	type	True	78.3587	477	1193	95	below_threshold
Nocardia asteroides	strain=ATCC 19247	GCA_005863255.1	1824	1824	suspected-type	True	77.2634	320	1193	95	below_threshold
Nocardia asteroides	strain=NBRC 15531	GCA_000308355.2	1824	1824	suspected-type	True	77.2433	323	1193	95	below_threshold
Nocardia asteroides	strain=DSM 43373	GCA_900114685.1	1824	1824	suspected-type	True	77.2271	324	1193	95	below_threshold
Nocardia asteroides	strain=NCTC11293	GCA_900637185.1	1824	1824	suspected-type	True	77.2126	332	1193	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	77.0406	331	1193	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:25:47,659] [INFO] DFAST Taxonomy check result was written to GCA_027592345.1_ASM2759234v1_genomic.fna/tc_result.tsv
[2023-06-29 04:25:47,660] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:25:47,660] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:25:47,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/checkm_data
[2023-06-29 04:25:47,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:25:47,704] [INFO] Task started: CheckM
[2023-06-29 04:25:47,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027592345.1_ASM2759234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027592345.1_ASM2759234v1_genomic.fna/checkm_input GCA_027592345.1_ASM2759234v1_genomic.fna/checkm_result
[2023-06-29 04:26:23,571] [INFO] Task succeeded: CheckM
[2023-06-29 04:26:23,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:26:23,595] [INFO] ===== Completeness check finished =====
[2023-06-29 04:26:23,595] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:26:23,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027592345.1_ASM2759234v1_genomic.fna/markers.fasta)
[2023-06-29 04:26:23,596] [INFO] Task started: Blastn
[2023-06-29 04:26:23,596] [INFO] Running command: blastn -query GCA_027592345.1_ASM2759234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e096f52-b877-485f-b0a1-a438b2df140c/dqc_reference/reference_markers_gtdb.fasta -out GCA_027592345.1_ASM2759234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:26:25,192] [INFO] Task succeeded: Blastn
[2023-06-29 04:26:25,197] [INFO] Selected 22 target genomes.
[2023-06-29 04:26:25,198] [INFO] Target genome list was writen to GCA_027592345.1_ASM2759234v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:26:25,208] [INFO] Task started: fastANI
[2023-06-29 04:26:25,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c428ea4-e563-4489-ae80-e4042f0ac606/GCA_027592345.1_ASM2759234v1_genomic.fna.gz --refList GCA_027592345.1_ASM2759234v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027592345.1_ASM2759234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:26:44,215] [INFO] Task succeeded: fastANI
[2023-06-29 04:26:44,237] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 04:26:44,237] [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
GCA_001510415.1	s__Mycobacterium sp001510415	99.5372	585	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005787665.1	s__Mycobacterium sp005787665	81.6565	596	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884065.1	s__Mycobacterium sp903884065	81.1974	779	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.70	0.92	0.92	2	-
GCA_017853185.1	s__Mycobacterium sp017853185	81.169	660	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018500045.1	s__Mycobacterium sp018500045	80.8471	462	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877095.1	s__Mycobacterium sp903877095	80.8099	701	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.96	99.94	0.97	0.96	4	-
GCA_018883075.1	s__Mycobacterium sp018883075	80.6745	505	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862565.1	s__Mycobacterium sp903862565	80.5881	631	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401645.1	s__Mycobacterium sp018401645	80.3974	556	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011694515.1	s__Mycobacterium sp011694515	80.1292	643	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	80.1214	693	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882965.1	s__Mycobacterium sp018882965	80.0124	629	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	79.5004	622	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_008329905.1	s__Mycobacterium sp008329905	79.3836	656	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	79.2065	542	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	79.0822	488	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	78.5927	527	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363795.1	s__Mycobacterium sp004363795	78.4988	471	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010730955.1	s__Mycobacterium aubagnense	78.3695	481	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_008709575.1	s__Mycobacterium sp008709575	77.8682	385	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637185.1	s__Nocardia asteroides	77.1966	334	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	5	-
GCF_001612885.1	s__Nocardia harenae	77.018	334	1193	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:26:44,239] [INFO] GTDB search result was written to GCA_027592345.1_ASM2759234v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:26:44,240] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:26:44,245] [INFO] DFAST_QC result json was written to GCA_027592345.1_ASM2759234v1_genomic.fna/dqc_result.json
[2023-06-29 04:26:44,245] [INFO] DFAST_QC completed!
[2023-06-29 04:26:44,246] [INFO] Total running time: 0h1m41s