[2024-01-24 13:58:55,698] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,701] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference
[2024-01-24 13:58:56,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:56,980] [INFO] Task started: Prodigal
[2024-01-24 13:58:56,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg62111acf-c974-4b87-9a34-a817af50d4fa/GCF_002982285.1_ASM298228v1_genomic.fna.gz | prodigal -d GCF_002982285.1_ASM298228v1_genomic.fna/cds.fna -a GCF_002982285.1_ASM298228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:10,275] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:10,276] [INFO] Task started: HMMsearch
[2024-01-24 13:59:10,276] [INFO] Running command: hmmsearch --tblout GCF_002982285.1_ASM298228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/reference_markers.hmm GCF_002982285.1_ASM298228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:10,553] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:10,554] [INFO] Found 6/6 markers.
[2024-01-24 13:59:10,595] [INFO] Query marker FASTA was written to GCF_002982285.1_ASM298228v1_genomic.fna/markers.fasta
[2024-01-24 13:59:10,596] [INFO] Task started: Blastn
[2024-01-24 13:59:10,596] [INFO] Running command: blastn -query GCF_002982285.1_ASM298228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/reference_markers.fasta -out GCF_002982285.1_ASM298228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:11,567] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:11,572] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:11,573] [INFO] Target genome list was writen to GCF_002982285.1_ASM298228v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:11,583] [INFO] Task started: fastANI
[2024-01-24 13:59:11,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg62111acf-c974-4b87-9a34-a817af50d4fa/GCF_002982285.1_ASM298228v1_genomic.fna.gz --refList GCF_002982285.1_ASM298228v1_genomic.fna/target_genomes.txt --output GCF_002982285.1_ASM298228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:22,355] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:22,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:22,356] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:22,366] [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 13:59:22,367] [INFO] Found 9 fastANI hits (9 hits with ANI > threshold)
[2024-01-24 13:59:22,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:22,367] [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 bovis	strain=ATCC 19210	GCA_002982285.1	1765	1773	type	True	100.0	1226	1242	95	conclusive
Mycobacterium tuberculosis variant caprae	strain=ATCC BAA-824	GCA_002982225.1	115862	1773	type	True	99.8936	1219	1242	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000277735.2	1773	1773	type	True	99.8774	1231	1242	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	99.8742	1233	1242	95	conclusive
Mycobacterium tuberculosis variant africanum	strain=ATCC 25420	GCA_002982335.1	33894	1773	type	True	99.856	1223	1242	95	conclusive
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	99.8555	1213	1242	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000667805.1	1773	1773	type	True	99.8517	1235	1242	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_003266045.1	1773	1773	type	True	99.8232	1203	1242	95	conclusive
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	99.7809	1139	1242	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,368] [INFO] DFAST Taxonomy check result was written to GCF_002982285.1_ASM298228v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:22,369] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:22,369] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:22,369] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/checkm_data
[2024-01-24 13:59:22,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:22,413] [INFO] Task started: CheckM
[2024-01-24 13:59:22,413] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002982285.1_ASM298228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002982285.1_ASM298228v1_genomic.fna/checkm_input GCF_002982285.1_ASM298228v1_genomic.fna/checkm_result
[2024-01-24 14:00:00,800] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:00,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:00,823] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:00,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:00,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002982285.1_ASM298228v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:00,824] [INFO] Task started: Blastn
[2024-01-24 14:00:00,824] [INFO] Running command: blastn -query GCF_002982285.1_ASM298228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf077a615-197d-4ab4-91ef-7d2c08790a83/dqc_reference/reference_markers_gtdb.fasta -out GCF_002982285.1_ASM298228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:02,201] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:02,205] [INFO] Selected 21 target genomes.
[2024-01-24 14:00:02,205] [INFO] Target genome list was writen to GCF_002982285.1_ASM298228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:02,230] [INFO] Task started: fastANI
[2024-01-24 14:00:02,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg62111acf-c974-4b87-9a34-a817af50d4fa/GCF_002982285.1_ASM298228v1_genomic.fna.gz --refList GCF_002982285.1_ASM298228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002982285.1_ASM298228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:25,493] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:25,514] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:25,515] [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	99.8742	1233	1242	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	85.9118	1004	1242	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	83.3368	961	1242	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	82.4055	972	1242	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	81.6719	813	1242	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	81.6657	880	1242	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	81.2354	852	1242	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	81.2329	883	1242	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	81.1173	744	1242	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	80.99	770	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_002086675.1	s__Mycobacterium persicum	80.9257	855	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_001667015.1	s__Mycobacterium sp001667015	80.9203	757	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	80.9179	861	1242	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	80.8997	780	1242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_900157385.1	s__Mycobacterium terramassiliense	80.7539	791	1242	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	80.7164	779	1242	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	80.4479	713	1242	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	80.1066	760	1242	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	79.8473	629	1242	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	79.6953	640	1242	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	78.1142	394	1242	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 14:00:25,517] [INFO] GTDB search result was written to GCF_002982285.1_ASM298228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:25,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:25,522] [INFO] DFAST_QC result json was written to GCF_002982285.1_ASM298228v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:25,522] [INFO] DFAST_QC completed!
[2024-01-24 14:00:25,522] [INFO] Total running time: 0h1m30s