[2024-01-25 19:43:20,467] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:20,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:20,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference
[2024-01-25 19:43:21,631] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:21,631] [INFO] Task started: Prodigal
[2024-01-25 19:43:21,632] [INFO] Running command: gunzip -c /var/lib/cwl/stga046a3bc-4864-4093-8460-0c67903c5a42/GCF_025821705.1_ASM2582170v1_genomic.fna.gz | prodigal -d GCF_025821705.1_ASM2582170v1_genomic.fna/cds.fna -a GCF_025821705.1_ASM2582170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:39,192] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:39,192] [INFO] Task started: HMMsearch
[2024-01-25 19:43:39,192] [INFO] Running command: hmmsearch --tblout GCF_025821705.1_ASM2582170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/reference_markers.hmm GCF_025821705.1_ASM2582170v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:39,463] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:39,464] [INFO] Found 6/6 markers.
[2024-01-25 19:43:39,515] [INFO] Query marker FASTA was written to GCF_025821705.1_ASM2582170v1_genomic.fna/markers.fasta
[2024-01-25 19:43:39,515] [INFO] Task started: Blastn
[2024-01-25 19:43:39,516] [INFO] Running command: blastn -query GCF_025821705.1_ASM2582170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/reference_markers.fasta -out GCF_025821705.1_ASM2582170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:40,681] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:40,684] [INFO] Selected 17 target genomes.
[2024-01-25 19:43:40,684] [INFO] Target genome list was writen to GCF_025821705.1_ASM2582170v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:40,693] [INFO] Task started: fastANI
[2024-01-25 19:43:40,693] [INFO] Running command: fastANI --query /var/lib/cwl/stga046a3bc-4864-4093-8460-0c67903c5a42/GCF_025821705.1_ASM2582170v1_genomic.fna.gz --refList GCF_025821705.1_ASM2582170v1_genomic.fna/target_genomes.txt --output GCF_025821705.1_ASM2582170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:00,794] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:00,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:00,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:00,805] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:44:00,806] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:00,806] [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
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	99.9952	2003	2006	95	conclusive
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	99.9924	2005	2006	95	conclusive
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	81.268	1075	2006	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.3623	909	2006	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.2617	876	2006	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.2294	925	2006	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.1842	934	2006	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.1546	706	2006	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.1196	866	2006	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.0608	873	2006	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.9196	621	2006	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4285	826	2006	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.2061	754	2006	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.0827	787	2006	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	78.9789	594	2006	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	78.742	641	2006	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	78.6702	635	2006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:00,807] [INFO] DFAST Taxonomy check result was written to GCF_025821705.1_ASM2582170v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:00,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:00,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:00,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/checkm_data
[2024-01-25 19:44:00,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:00,865] [INFO] Task started: CheckM
[2024-01-25 19:44:00,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821705.1_ASM2582170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821705.1_ASM2582170v1_genomic.fna/checkm_input GCF_025821705.1_ASM2582170v1_genomic.fna/checkm_result
[2024-01-25 19:45:23,647] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:23,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:23,667] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:23,667] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:23,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821705.1_ASM2582170v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:23,668] [INFO] Task started: Blastn
[2024-01-25 19:45:23,668] [INFO] Running command: blastn -query GCF_025821705.1_ASM2582170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg52e0a535-7099-428d-9a44-a596bc9d5999/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821705.1_ASM2582170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:25,482] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:25,485] [INFO] Selected 18 target genomes.
[2024-01-25 19:45:25,485] [INFO] Target genome list was writen to GCF_025821705.1_ASM2582170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:25,498] [INFO] Task started: fastANI
[2024-01-25 19:45:25,499] [INFO] Running command: fastANI --query /var/lib/cwl/stga046a3bc-4864-4093-8460-0c67903c5a42/GCF_025821705.1_ASM2582170v1_genomic.fna.gz --refList GCF_025821705.1_ASM2582170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821705.1_ASM2582170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:47,893] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:47,905] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:47,905] [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_010725885.1	s__Mycobacterium tokaiense	99.9952	2003	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	96.52	0.94	0.90	4	conclusive
GCF_001984215.1	s__Mycobacterium sp001984215	84.6639	1424	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015710575.1	s__Mycobacterium sp015710575	81.2903	1071	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	-
GCF_002592005.1	s__Mycobacterium palauense	80.4146	901	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	80.2631	883	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.1531	939	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_010726955.1	s__Mycobacterium fallax	80.1347	709	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_010731695.1	s__Mycobacterium litorale	80.0842	874	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001499995.1	s__Mycobacterium sp001499995	79.9227	808	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197405.1	s__Mycobacterium sp016197405	79.9113	901	2006	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	79.8128	878	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	79.7394	855	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018326285.1	s__Mycobacterium sp018326285	79.4971	757	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002250655.1	s__Mycobacterium sphagni	79.2149	753	2006	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	79.0807	788	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667275.1	s__Mycobacterium sp001667275	79.0797	669	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.42	96.39	0.93	0.93	5	-
GCF_002101585.1	s__Mycobacterium engbaekii	78.9902	593	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_002102155.1	s__Mycobacterium europaeum	78.9559	669	2006	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:47,906] [INFO] GTDB search result was written to GCF_025821705.1_ASM2582170v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:47,907] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:47,910] [INFO] DFAST_QC result json was written to GCF_025821705.1_ASM2582170v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:47,911] [INFO] DFAST_QC completed!
[2024-01-25 19:45:47,911] [INFO] Total running time: 0h2m27s