[2024-01-24 12:14:33,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,998] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,998] [INFO] DQC Reference Directory: /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference
[2024-01-24 12:14:35,396] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,398] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a544bbe-99f0-454c-aa79-e93b7d0397d1/GCF_025822245.1_ASM2582224v1_genomic.fna.gz | prodigal -d GCF_025822245.1_ASM2582224v1_genomic.fna/cds.fna -a GCF_025822245.1_ASM2582224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:56,732] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:56,733] [INFO] Task started: HMMsearch
[2024-01-24 12:14:56,733] [INFO] Running command: hmmsearch --tblout GCF_025822245.1_ASM2582224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/reference_markers.hmm GCF_025822245.1_ASM2582224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:57,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:57,127] [INFO] Found 6/6 markers.
[2024-01-24 12:14:57,188] [INFO] Query marker FASTA was written to GCF_025822245.1_ASM2582224v1_genomic.fna/markers.fasta
[2024-01-24 12:14:57,189] [INFO] Task started: Blastn
[2024-01-24 12:14:57,189] [INFO] Running command: blastn -query GCF_025822245.1_ASM2582224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/reference_markers.fasta -out GCF_025822245.1_ASM2582224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:58,405] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:58,409] [INFO] Selected 32 target genomes.
[2024-01-24 12:14:58,410] [INFO] Target genome list was writen to GCF_025822245.1_ASM2582224v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:58,421] [INFO] Task started: fastANI
[2024-01-24 12:14:58,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a544bbe-99f0-454c-aa79-e93b7d0397d1/GCF_025822245.1_ASM2582224v1_genomic.fna.gz --refList GCF_025822245.1_ASM2582224v1_genomic.fna/target_genomes.txt --output GCF_025822245.1_ASM2582224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:34,476] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:34,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:34,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:34,512] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:34,512] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:34,512] [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 arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	81.1487	1157	2137	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	81.001	1134	2137	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.1942	936	2137	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.156	954	2137	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	79.9871	945	2137	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	79.9458	808	2137	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	79.7591	909	2137	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.7576	816	2137	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	79.7086	948	2137	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	79.6785	952	2137	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	79.6739	842	2137	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.6573	953	2137	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	79.6568	933	2137	95	below_threshold
Mycolicibacterium tokaiense	strain=NCTC10821	GCA_900453365.1	39695	39695	suspected-type	True	79.6238	876	2137	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	79.5949	881	2137	95	below_threshold
Mycolicibacterium tokaiense	strain=JCM 6373	GCA_010725885.1	39695	39695	suspected-type	True	79.563	894	2137	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	79.5349	870	2137	95	below_threshold
Mycolicibacterium wolinskyi	strain=ATCC 700010	GCA_002101965.1	59750	59750	type	True	79.4971	936	2137	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	79.4745	660	2137	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.4506	668	2137	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.3723	900	2137	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.3207	818	2137	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	79.3059	786	2137	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	79.2765	840	2137	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.128	828	2137	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	78.9798	661	2137	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	78.9789	651	2137	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	78.88	663	2137	95	below_threshold
Mycobacterium stomatepiae	strain=JCM 17783	GCA_010731715.1	470076	470076	type	True	78.593	606	2137	95	below_threshold
Mycobacterium ahvazicum	strain=AFP003	GCA_900176255.2	1964395	1964395	type	True	78.5259	652	2137	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	78.2145	535	2137	95	below_threshold
Mycobacterium pseudokansasii	strain=MK142	GCA_900566075.1	2341080	2341080	type	True	77.9991	553	2137	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:34,516] [INFO] DFAST Taxonomy check result was written to GCF_025822245.1_ASM2582224v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:34,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:34,517] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:34,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/checkm_data
[2024-01-24 12:15:34,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:34,582] [INFO] Task started: CheckM
[2024-01-24 12:15:34,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822245.1_ASM2582224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822245.1_ASM2582224v1_genomic.fna/checkm_input GCF_025822245.1_ASM2582224v1_genomic.fna/checkm_result
[2024-01-24 12:16:40,573] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:40,574] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,599] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:40,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:40,600] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822245.1_ASM2582224v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:40,601] [INFO] Task started: Blastn
[2024-01-24 12:16:40,601] [INFO] Running command: blastn -query GCF_025822245.1_ASM2582224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1d640f9-185f-48eb-bf76-d2cbee10980c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822245.1_ASM2582224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:42,325] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:42,330] [INFO] Selected 20 target genomes.
[2024-01-24 12:16:42,330] [INFO] Target genome list was writen to GCF_025822245.1_ASM2582224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:42,346] [INFO] Task started: fastANI
[2024-01-24 12:16:42,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a544bbe-99f0-454c-aa79-e93b7d0397d1/GCF_025822245.1_ASM2582224v1_genomic.fna.gz --refList GCF_025822245.1_ASM2582224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822245.1_ASM2582224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:08,743] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:08,761] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:08,762] [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_008329535.1	s__Mycobacterium sp008329535	89.872	1694	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	88.5126	1600	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCF_001426545.1	s__Mycobacterium sp001426545	88.3503	1652	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016462545.1	s__Mycobacterium sp016462545	83.2395	1238	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	82.6837	1250	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439015.1	s__Mycobacterium hodleri_A	82.4986	1203	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731815.2	s__Mycobacterium arabiense	81.162	1154	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731735.1	s__Mycobacterium sediminis	81.0443	1163	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329605.1	s__Mycobacterium sp008329605	80.9177	1162	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202335.1	s__Mycobacterium sp014202335	80.7785	1178	2137	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	80.3326	975	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	80.2998	863	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_003284965.1	s__Mycobacterium sp003284965	80.1596	801	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	79.9031	938	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_018326285.1	s__Mycobacterium sp018326285	79.8722	879	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002592005.1	s__Mycobacterium palauense	79.7606	870	2137	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	79.423	894	2137	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	79.079	749	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673535.1	s__Mycobacterium sp001673535	78.9477	683	2137	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	78.561	640	2137	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 12:17:08,764] [INFO] GTDB search result was written to GCF_025822245.1_ASM2582224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:08,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:08,770] [INFO] DFAST_QC result json was written to GCF_025822245.1_ASM2582224v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:08,770] [INFO] DFAST_QC completed!
[2024-01-24 12:17:08,771] [INFO] Total running time: 0h2m35s