[2024-01-24 11:43:52,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference
[2024-01-24 11:43:53,799] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:53,800] [INFO] Task started: Prodigal
[2024-01-24 11:43:53,800] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe7b5cbc-3ebb-402d-ba38-8553265209aa/GCF_002982335.1_ASM298233v1_genomic.fna.gz | prodigal -d GCF_002982335.1_ASM298233v1_genomic.fna/cds.fna -a GCF_002982335.1_ASM298233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:07,865] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:07,866] [INFO] Task started: HMMsearch
[2024-01-24 11:44:07,866] [INFO] Running command: hmmsearch --tblout GCF_002982335.1_ASM298233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/reference_markers.hmm GCF_002982335.1_ASM298233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:08,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:08,084] [INFO] Found 6/6 markers.
[2024-01-24 11:44:08,119] [INFO] Query marker FASTA was written to GCF_002982335.1_ASM298233v1_genomic.fna/markers.fasta
[2024-01-24 11:44:08,120] [INFO] Task started: Blastn
[2024-01-24 11:44:08,120] [INFO] Running command: blastn -query GCF_002982335.1_ASM298233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/reference_markers.fasta -out GCF_002982335.1_ASM298233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:09,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:09,042] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:09,042] [INFO] Target genome list was writen to GCF_002982335.1_ASM298233v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:09,046] [INFO] Task started: fastANI
[2024-01-24 11:44:09,046] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7b5cbc-3ebb-402d-ba38-8553265209aa/GCF_002982335.1_ASM298233v1_genomic.fna.gz --refList GCF_002982335.1_ASM298233v1_genomic.fna/target_genomes.txt --output GCF_002982335.1_ASM298233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:19,794] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:19,794] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:19,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:19,803] [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 11:44:19,803] [INFO] Found 8 fastANI hits (8 hits with ANI > threshold)
[2024-01-24 11:44:19,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:19,804] [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 variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	100.0	1396	1399	95	conclusive
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	99.8977	1356	1399	95	conclusive
Mycobacterium tuberculosis variant caprae	strain=ATCC BAA-824	GCA_002982225.1	115862	1773	type	True	99.8817	1350	1399	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	99.8773	1388	1399	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	99.8729	1388	1399	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	99.8644	1337	1399	95	conclusive
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	99.7726	1253	1399	95	conclusive
Mycobacterium tuberculosis variant bovis	strain=ATCC 19210	GCA_002982285.1	1765	1773	type	True	99.7155	1204	1399	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:44:19,805] [INFO] DFAST Taxonomy check result was written to GCF_002982335.1_ASM298233v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:19,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:19,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:19,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/checkm_data
[2024-01-24 11:44:19,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:19,848] [INFO] Task started: CheckM
[2024-01-24 11:44:19,848] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002982335.1_ASM298233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002982335.1_ASM298233v1_genomic.fna/checkm_input GCF_002982335.1_ASM298233v1_genomic.fna/checkm_result
[2024-01-24 11:45:01,511] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:01,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:01,529] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:01,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:01,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002982335.1_ASM298233v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:01,530] [INFO] Task started: Blastn
[2024-01-24 11:45:01,530] [INFO] Running command: blastn -query GCF_002982335.1_ASM298233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1b2976c-845b-4a84-ab0c-cad942f6d9d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002982335.1_ASM298233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:02,827] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:02,830] [INFO] Selected 21 target genomes.
[2024-01-24 11:45:02,830] [INFO] Target genome list was writen to GCF_002982335.1_ASM298233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:02,843] [INFO] Task started: fastANI
[2024-01-24 11:45:02,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7b5cbc-3ebb-402d-ba38-8553265209aa/GCF_002982335.1_ASM298233v1_genomic.fna.gz --refList GCF_002982335.1_ASM298233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002982335.1_ASM298233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:27,100] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:27,116] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:27,116] [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	99.8729	1388	1399	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	85.9502	1101	1399	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	83.5023	1036	1399	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	82.5676	1053	1399	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	81.7211	887	1399	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	81.6265	1009	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900566055.1	s__Mycobacterium innocens	81.2465	936	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.1854	974	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_001954195.1	s__Mycobacterium sp001954195	81.0998	827	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.85	0.97	0.97	2	-
GCF_002086635.1	s__Mycobacterium alsense	81.0972	838	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001667015.1	s__Mycobacterium sp001667015	80.9824	833	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	80.9817	845	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_002086675.1	s__Mycobacterium persicum	80.9451	945	1399	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	80.9284	962	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.8813	868	1399	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.8677	848	1399	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	80.58	780	1399	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	80.2295	823	1399	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	79.8426	694	1399	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	79.8301	718	1399	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	78.0633	428	1399	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 11:45:27,118] [INFO] GTDB search result was written to GCF_002982335.1_ASM298233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:27,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:27,126] [INFO] DFAST_QC result json was written to GCF_002982335.1_ASM298233v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:27,127] [INFO] DFAST_QC completed!
[2024-01-24 11:45:27,127] [INFO] Total running time: 0h1m35s