[2024-01-24 15:19:04,443] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,445] [INFO] DQC Reference Directory: /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference
[2024-01-24 15:19:05,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,671] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,671] [INFO] Running command: gunzip -c /var/lib/cwl/stgc30025af-9bfd-493d-ac31-7a6aad31b373/GCF_900078685.2_PRJEB13234_genomic.fna.gz | prodigal -d GCF_900078685.2_PRJEB13234_genomic.fna/cds.fna -a GCF_900078685.2_PRJEB13234_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:21,272] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:21,273] [INFO] Task started: HMMsearch
[2024-01-24 15:19:21,273] [INFO] Running command: hmmsearch --tblout GCF_900078685.2_PRJEB13234_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/reference_markers.hmm GCF_900078685.2_PRJEB13234_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:21,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:21,560] [INFO] Found 6/6 markers.
[2024-01-24 15:19:21,614] [INFO] Query marker FASTA was written to GCF_900078685.2_PRJEB13234_genomic.fna/markers.fasta
[2024-01-24 15:19:21,615] [INFO] Task started: Blastn
[2024-01-24 15:19:21,615] [INFO] Running command: blastn -query GCF_900078685.2_PRJEB13234_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/reference_markers.fasta -out GCF_900078685.2_PRJEB13234_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:22,718] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:22,721] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:22,721] [INFO] Target genome list was writen to GCF_900078685.2_PRJEB13234_genomic.fna/target_genomes.txt
[2024-01-24 15:19:22,728] [INFO] Task started: fastANI
[2024-01-24 15:19:22,729] [INFO] Running command: fastANI --query /var/lib/cwl/stgc30025af-9bfd-493d-ac31-7a6aad31b373/GCF_900078685.2_PRJEB13234_genomic.fna.gz --refList GCF_900078685.2_PRJEB13234_genomic.fna/target_genomes.txt --output GCF_900078685.2_PRJEB13234_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:45,637] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:45,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:45,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:45,660] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:45,660] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:45,660] [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
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	88.4747	1108	1595	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	86.431	1119	1595	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	86.0282	1080	1595	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	85.9529	1125	1595	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	85.9033	1080	1595	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	85.8171	1107	1595	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	85.81	1095	1595	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	85.7605	1111	1595	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	85.1265	1030	1595	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	85.0838	1088	1595	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	84.5993	1095	1595	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	84.5265	1079	1595	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	79.8381	678	1595	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.3393	636	1595	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.1599	612	1595	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.1085	622	1595	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	78.7887	635	1595	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	78.6014	540	1595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:45,662] [INFO] DFAST Taxonomy check result was written to GCF_900078685.2_PRJEB13234_genomic.fna/tc_result.tsv
[2024-01-24 15:19:45,662] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:45,663] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:45,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/checkm_data
[2024-01-24 15:19:45,664] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:45,716] [INFO] Task started: CheckM
[2024-01-24 15:19:45,717] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900078685.2_PRJEB13234_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900078685.2_PRJEB13234_genomic.fna/checkm_input GCF_900078685.2_PRJEB13234_genomic.fna/checkm_result
[2024-01-24 15:20:31,567] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:31,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:31,592] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:31,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:31,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900078685.2_PRJEB13234_genomic.fna/markers.fasta)
[2024-01-24 15:20:31,593] [INFO] Task started: Blastn
[2024-01-24 15:20:31,593] [INFO] Running command: blastn -query GCF_900078685.2_PRJEB13234_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5a60e-21e6-4063-8001-2069c4a1b57d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900078685.2_PRJEB13234_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:33,261] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:33,265] [INFO] Selected 16 target genomes.
[2024-01-24 15:20:33,265] [INFO] Target genome list was writen to GCF_900078685.2_PRJEB13234_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:33,352] [INFO] Task started: fastANI
[2024-01-24 15:20:33,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgc30025af-9bfd-493d-ac31-7a6aad31b373/GCF_900078685.2_PRJEB13234_genomic.fna.gz --refList GCF_900078685.2_PRJEB13234_genomic.fna/target_genomes_gtdb.txt --output GCF_900078685.2_PRJEB13234_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:52,519] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:52,546] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:52,547] [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_900078685.2	s__Mycobacterium icosiumassiliensis	100.0	1590	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001673105.1	s__Mycobacterium heraklionense_A	90.4911	1207	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	90.1651	1227	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	89.798	1150	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	88.4961	1106	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_002101585.1	s__Mycobacterium engbaekii	86.0459	1079	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_010731755.1	s__Mycobacterium minnesotense	85.9565	1125	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010729485.1	s__Mycobacterium hiberniae	85.8429	1104	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_002086515.1	s__Mycobacterium arupense	85.77	1110	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCF_002086285.1	s__Mycobacterium kumamotonense	85.1056	1086	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_001667945.1	s__Mycobacterium sinense_B	84.9917	1068	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_002086455.1	s__Mycobacterium algericum	84.6756	1054	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_018455725.1	s__Mycobacterium sp018455725	82.389	931	1595	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	79.3736	628	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001245615.1	s__Mycobacterium neworleansense	79.2842	659	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013390125.1	s__Mycobacterium hippocampi_A	78.5559	562	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:52,549] [INFO] GTDB search result was written to GCF_900078685.2_PRJEB13234_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:52,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:52,556] [INFO] DFAST_QC result json was written to GCF_900078685.2_PRJEB13234_genomic.fna/dqc_result.json
[2024-01-24 15:20:52,556] [INFO] DFAST_QC completed!
[2024-01-24 15:20:52,556] [INFO] Total running time: 0h1m48s