[2024-01-25 18:12:20,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:20,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:20,559] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference
[2024-01-25 18:12:21,685] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:21,685] [INFO] Task started: Prodigal
[2024-01-25 18:12:21,685] [INFO] Running command: gunzip -c /var/lib/cwl/stged5f6940-7c0b-4c78-b974-5e01f3d3dce2/GCF_025822305.1_ASM2582230v1_genomic.fna.gz | prodigal -d GCF_025822305.1_ASM2582230v1_genomic.fna/cds.fna -a GCF_025822305.1_ASM2582230v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:43,489] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:43,489] [INFO] Task started: HMMsearch
[2024-01-25 18:12:43,489] [INFO] Running command: hmmsearch --tblout GCF_025822305.1_ASM2582230v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/reference_markers.hmm GCF_025822305.1_ASM2582230v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:43,812] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:43,813] [INFO] Found 6/6 markers.
[2024-01-25 18:12:43,869] [INFO] Query marker FASTA was written to GCF_025822305.1_ASM2582230v1_genomic.fna/markers.fasta
[2024-01-25 18:12:43,869] [INFO] Task started: Blastn
[2024-01-25 18:12:43,869] [INFO] Running command: blastn -query GCF_025822305.1_ASM2582230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/reference_markers.fasta -out GCF_025822305.1_ASM2582230v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:45,084] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:45,088] [INFO] Selected 24 target genomes.
[2024-01-25 18:12:45,088] [INFO] Target genome list was writen to GCF_025822305.1_ASM2582230v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:45,115] [INFO] Task started: fastANI
[2024-01-25 18:12:45,116] [INFO] Running command: fastANI --query /var/lib/cwl/stged5f6940-7c0b-4c78-b974-5e01f3d3dce2/GCF_025822305.1_ASM2582230v1_genomic.fna.gz --refList GCF_025822305.1_ASM2582230v1_genomic.fna/target_genomes.txt --output GCF_025822305.1_ASM2582230v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:14,470] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:14,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:14,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:14,483] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:13:14,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:13:14,484] [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	98.018	1903	2215	95	conclusive
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	97.9762	1912	2215	95	conclusive
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	81.2955	1131	2215	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.787	739	2215	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.7157	761	2215	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.42	948	2215	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.362	940	2215	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	80.3086	965	2215	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	80.2701	977	2215	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.22	914	2215	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.2134	941	2215	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	80.0453	647	2215	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.9903	937	2215	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.9401	842	2215	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.6318	800	2215	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5709	857	2215	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.5573	775	2215	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4478	821	2215	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.396	778	2215	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	79.2168	686	2215	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	79.207	677	2215	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.1832	800	2215	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	78.8885	619	2215	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	78.831	618	2215	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:14,485] [INFO] DFAST Taxonomy check result was written to GCF_025822305.1_ASM2582230v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:14,486] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:14,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:14,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/checkm_data
[2024-01-25 18:13:14,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:14,548] [INFO] Task started: CheckM
[2024-01-25 18:13:14,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822305.1_ASM2582230v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822305.1_ASM2582230v1_genomic.fna/checkm_input GCF_025822305.1_ASM2582230v1_genomic.fna/checkm_result
[2024-01-25 18:14:52,963] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:52,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:52,984] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:52,985] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:52,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822305.1_ASM2582230v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:52,986] [INFO] Task started: Blastn
[2024-01-25 18:14:52,986] [INFO] Running command: blastn -query GCF_025822305.1_ASM2582230v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeaa9aaa-36f2-4267-82c8-817b60af19ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822305.1_ASM2582230v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:55,035] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:55,043] [INFO] Selected 21 target genomes.
[2024-01-25 18:14:55,043] [INFO] Target genome list was writen to GCF_025822305.1_ASM2582230v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:55,093] [INFO] Task started: fastANI
[2024-01-25 18:14:55,093] [INFO] Running command: fastANI --query /var/lib/cwl/stged5f6940-7c0b-4c78-b974-5e01f3d3dce2/GCF_025822305.1_ASM2582230v1_genomic.fna.gz --refList GCF_025822305.1_ASM2582230v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822305.1_ASM2582230v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:15:21,388] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:21,401] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:15:21,401] [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	98.0289	1902	2215	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	84.6992	1513	2215	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	81.2842	1133	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.09	99.09	0.96	0.96	2	-
GCF_010726955.1	s__Mycobacterium fallax	80.7077	762	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_002592005.1	s__Mycobacterium palauense	80.4649	939	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	80.2637	979	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_001545925.1	s__Mycobacterium sp001545925	80.2379	818	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	80.2292	938	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086115.1	s__Mycobacterium bacteremicum	80.1583	952	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499995.1	s__Mycobacterium sp001499995	80.0092	862	2215	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	79.986	894	2215	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	79.9107	884	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	79.701	901	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004745805.1	s__Mycobacterium sp004745805	79.646	823	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250655.1	s__Mycobacterium sphagni	79.4005	776	2215	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	79.2293	794	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	79.2044	678	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_001667505.1	s__Mycobacterium sp001667505	79.1816	808	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157375.1	s__Mycobacterium rhizamassiliense	79.0744	681	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667585.1	s__Mycobacterium sp001667585	78.9004	629	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	77.4672	426	2215	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:15:21,402] [INFO] GTDB search result was written to GCF_025822305.1_ASM2582230v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:15:21,403] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:15:21,407] [INFO] DFAST_QC result json was written to GCF_025822305.1_ASM2582230v1_genomic.fna/dqc_result.json
[2024-01-25 18:15:21,407] [INFO] DFAST_QC completed!
[2024-01-25 18:15:21,407] [INFO] Total running time: 0h3m1s