[2024-01-24 12:37:24,449] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,451] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference
[2024-01-24 12:37:25,796] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:25,797] [INFO] Task started: Prodigal
[2024-01-24 12:37:25,797] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8079fbe-ff95-409b-bf6d-954550b06960/GCF_002592005.1_ASM259200v1_genomic.fna.gz | prodigal -d GCF_002592005.1_ASM259200v1_genomic.fna/cds.fna -a GCF_002592005.1_ASM259200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:43,695] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:43,695] [INFO] Task started: HMMsearch
[2024-01-24 12:37:43,696] [INFO] Running command: hmmsearch --tblout GCF_002592005.1_ASM259200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/reference_markers.hmm GCF_002592005.1_ASM259200v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:43,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:44,000] [INFO] Found 6/6 markers.
[2024-01-24 12:37:44,053] [INFO] Query marker FASTA was written to GCF_002592005.1_ASM259200v1_genomic.fna/markers.fasta
[2024-01-24 12:37:44,054] [INFO] Task started: Blastn
[2024-01-24 12:37:44,054] [INFO] Running command: blastn -query GCF_002592005.1_ASM259200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/reference_markers.fasta -out GCF_002592005.1_ASM259200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:45,297] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:45,300] [INFO] Selected 28 target genomes.
[2024-01-24 12:37:45,301] [INFO] Target genome list was writen to GCF_002592005.1_ASM259200v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:45,315] [INFO] Task started: fastANI
[2024-01-24 12:37:45,315] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8079fbe-ff95-409b-bf6d-954550b06960/GCF_002592005.1_ASM259200v1_genomic.fna.gz --refList GCF_002592005.1_ASM259200v1_genomic.fna/target_genomes.txt --output GCF_002592005.1_ASM259200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:17,835] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:17,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:17,837] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:17,868] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:38:17,869] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:17,869] [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
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	100.0	1954	1965	95	conclusive
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.3292	982	1965	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	81.3141	978	1965	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	81.2307	818	1965	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	81.2288	820	1965	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.0416	952	1965	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.5798	690	1965	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	80.4667	924	1965	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.4661	928	1965	95	below_threshold
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	80.4446	922	1965	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	80.4122	972	1965	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	80.2914	875	1965	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	80.2444	884	1965	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.9743	832	1965	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	79.959	867	1965	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8495	907	1965	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7029	904	1965	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.6603	879	1965	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.6305	882	1965	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	79.6174	734	1965	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	79.5823	858	1965	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.5709	892	1965	95	below_threshold
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	79.5235	749	1965	95	below_threshold
Mycobacterium parmense	strain=JCM 14742	GCA_010730575.1	185642	185642	type	True	79.4764	739	1965	95	below_threshold
Mycobacterium parmense	strain=DSM 44553	GCA_002102335.1	185642	185642	type	True	79.4603	755	1965	95	below_threshold
Gordonia desulfuricans	strain=NBRC 100010	GCA_001485495.1	89051	89051	type	True	77.6472	475	1965	95	below_threshold
Gordonia desulfuricans	strain=213E	GCA_010119475.1	89051	89051	type	True	77.6347	483	1965	95	below_threshold
Prescottella defluvii	strain=Ca11	GCA_000738775.1	1323361	1323361	type	True	77.4682	429	1965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:17,871] [INFO] DFAST Taxonomy check result was written to GCF_002592005.1_ASM259200v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:17,871] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:17,871] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:17,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/checkm_data
[2024-01-24 12:38:17,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:17,929] [INFO] Task started: CheckM
[2024-01-24 12:38:17,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002592005.1_ASM259200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002592005.1_ASM259200v1_genomic.fna/checkm_input GCF_002592005.1_ASM259200v1_genomic.fna/checkm_result
[2024-01-24 12:39:22,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:22,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:22,096] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:22,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:22,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002592005.1_ASM259200v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:22,098] [INFO] Task started: Blastn
[2024-01-24 12:39:22,098] [INFO] Running command: blastn -query GCF_002592005.1_ASM259200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ed0a00d-fe94-4acb-9652-7c1f98a8d749/dqc_reference/reference_markers_gtdb.fasta -out GCF_002592005.1_ASM259200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:23,808] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:23,813] [INFO] Selected 28 target genomes.
[2024-01-24 12:39:23,813] [INFO] Target genome list was writen to GCF_002592005.1_ASM259200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:23,836] [INFO] Task started: fastANI
[2024-01-24 12:39:23,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8079fbe-ff95-409b-bf6d-954550b06960/GCF_002592005.1_ASM259200v1_genomic.fna.gz --refList GCF_002592005.1_ASM259200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002592005.1_ASM259200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:56,942] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:56,966] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:39:56,967] [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_002592005.1	s__Mycobacterium palauense	100.0	1954	1965	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_900637205.1	s__Mycobacterium chitae	81.3238	983	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010726955.1	s__Mycobacterium fallax	81.2218	818	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_001583415.1	s__Mycobacterium phlei	80.9721	954	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_010725885.1	s__Mycobacterium tokaiense	80.4556	925	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	-
GCF_900108565.1	s__Mycobacterium rutilum	80.4311	935	1965	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	80.4089	855	1965	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	80.3983	937	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.3395	961	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001500125.1	s__Mycobacterium sp001500125	80.221	881	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007745.1	s__Mycobacterium litorale_A	80.2209	875	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853185.1	s__Mycobacterium sp017853185	80.165	579	1965	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	80.162	961	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499965.1	s__Mycobacterium sp001499965	80.1361	943	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457595.1	s__Mycobacterium smegmatis	79.9951	906	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_001570485.1	s__Mycobacterium novocastrense	79.9865	858	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_004014805.1	s__Mycobacterium elephantis	79.9813	832	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_004745805.1	s__Mycobacterium sp004745805	79.9668	866	1965	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	79.9558	867	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284965.1	s__Mycobacterium sp003284965	79.9152	775	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984215.1	s__Mycobacterium sp001984215	79.7508	912	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	79.6239	883	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	79.5768	893	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	79.5633	802	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	79.4902	776	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730575.1	s__Mycobacterium parmense	79.4751	740	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667505.1	s__Mycobacterium sp001667505	79.4443	818	1965	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370645.1	s__Mycobacterium simiae_A	78.119	498	1965	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 12:39:56,969] [INFO] GTDB search result was written to GCF_002592005.1_ASM259200v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:56,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:56,974] [INFO] DFAST_QC result json was written to GCF_002592005.1_ASM259200v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:56,974] [INFO] DFAST_QC completed!
[2024-01-24 12:39:56,974] [INFO] Total running time: 0h2m33s