[2024-01-24 14:30:59,583] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference
[2024-01-24 14:31:01,018] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:01,020] [INFO] Task started: Prodigal
[2024-01-24 14:31:01,020] [INFO] Running command: gunzip -c /var/lib/cwl/stg220e0242-973a-4532-8005-468d0e15edd2/GCF_003266045.1_ASM326604v1_genomic.fna.gz | prodigal -d GCF_003266045.1_ASM326604v1_genomic.fna/cds.fna -a GCF_003266045.1_ASM326604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:16,738] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:16,738] [INFO] Task started: HMMsearch
[2024-01-24 14:31:16,739] [INFO] Running command: hmmsearch --tblout GCF_003266045.1_ASM326604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/reference_markers.hmm GCF_003266045.1_ASM326604v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,037] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,039] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,080] [INFO] Query marker FASTA was written to GCF_003266045.1_ASM326604v1_genomic.fna/markers.fasta
[2024-01-24 14:31:17,081] [INFO] Task started: Blastn
[2024-01-24 14:31:17,081] [INFO] Running command: blastn -query GCF_003266045.1_ASM326604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/reference_markers.fasta -out GCF_003266045.1_ASM326604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,139] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,143] [INFO] Selected 6 target genomes.
[2024-01-24 14:31:18,144] [INFO] Target genome list was writen to GCF_003266045.1_ASM326604v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,155] [INFO] Task started: fastANI
[2024-01-24 14:31:18,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg220e0242-973a-4532-8005-468d0e15edd2/GCF_003266045.1_ASM326604v1_genomic.fna.gz --refList GCF_003266045.1_ASM326604v1_genomic.fna/target_genomes.txt --output GCF_003266045.1_ASM326604v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:27,000] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:27,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:27,001] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:27,010] [WARNING] Following organisms are indistinguishable with ANI. [Mycobacterium tuberculosis(1773), Mycobacterium tuberculosis variant bovis(1765), Mycobacterium tuberculosis variant microti(1806), Mycobacterium tuberculosis variant africanum(33894), Mycobacterium tuberculosis variant caprae(115862), Mycobacterium tuberculosis variant pinnipedii(194542)]
[2024-01-24 14:31:27,011] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:31:27,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:27,011] [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 tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	100.0	1381	1384	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000277735.2	1773	1773	type	True	99.99	1383	1384	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	99.9888	1383	1384	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	99.9761	1380	1384	95	conclusive
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	99.8633	1332	1384	95	conclusive
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	99.8086	1239	1384	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:31:27,013] [INFO] DFAST Taxonomy check result was written to GCF_003266045.1_ASM326604v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:27,013] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:27,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:27,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/checkm_data
[2024-01-24 14:31:27,016] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:27,064] [INFO] Task started: CheckM
[2024-01-24 14:31:27,065] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003266045.1_ASM326604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003266045.1_ASM326604v1_genomic.fna/checkm_input GCF_003266045.1_ASM326604v1_genomic.fna/checkm_result
[2024-01-24 14:32:12,445] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:12,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:12,464] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:12,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:12,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003266045.1_ASM326604v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:12,466] [INFO] Task started: Blastn
[2024-01-24 14:32:12,466] [INFO] Running command: blastn -query GCF_003266045.1_ASM326604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39783fed-33f6-452b-bf94-01f11f085d16/dqc_reference/reference_markers_gtdb.fasta -out GCF_003266045.1_ASM326604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:13,871] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:13,874] [INFO] Selected 21 target genomes.
[2024-01-24 14:32:13,874] [INFO] Target genome list was writen to GCF_003266045.1_ASM326604v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:13,897] [INFO] Task started: fastANI
[2024-01-24 14:32:13,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg220e0242-973a-4532-8005-468d0e15edd2/GCF_003266045.1_ASM326604v1_genomic.fna.gz --refList GCF_003266045.1_ASM326604v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003266045.1_ASM326604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:39,441] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:39,461] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:39,462] [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_000195955.2	s__Mycobacterium tuberculosis	99.9888	1383	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	conclusive
GCF_002104675.1	s__Mycobacterium decipiens	85.9944	1105	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	83.5143	1037	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010731535.1	s__Mycobacterium lacus	82.5756	1047	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	81.7648	877	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002101845.1	s__Mycobacterium riyadhense	81.6743	996	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.2684	971	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900566055.1	s__Mycobacterium innocens	81.2547	914	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.1241	820	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954195.1	s__Mycobacterium sp001954195	81.1055	822	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_002086675.1	s__Mycobacterium persicum	81.0864	921	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	81.0304	949	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002101815.1	s__Mycobacterium paraense	80.9947	847	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_002086635.1	s__Mycobacterium alsense	80.9363	838	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.8593	845	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.843	855	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007714205.1	s__Mycobacterium helveticum	80.5788	783	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003614435.1	s__Mycobacterium paragordonae	80.1096	832	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_002101735.1	s__Mycobacterium kyorinense	79.8972	673	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002101595.1	s__Mycobacterium celatum	79.6759	715	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001499905.1	s__Mycobacterium sp001499905	78.1479	414	1384	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 14:32:39,464] [INFO] GTDB search result was written to GCF_003266045.1_ASM326604v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:39,464] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:39,468] [INFO] DFAST_QC result json was written to GCF_003266045.1_ASM326604v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:39,468] [INFO] DFAST_QC completed!
[2024-01-24 14:32:39,468] [INFO] Total running time: 0h1m40s