[2024-01-24 11:51:10,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,102] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference
[2024-01-24 11:51:11,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,413] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg46e98116-7815-4520-baad-9f805011da6c/GCF_000974705.1_ASM97470v1_genomic.fna.gz | prodigal -d GCF_000974705.1_ASM97470v1_genomic.fna/cds.fna -a GCF_000974705.1_ASM97470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:25,071] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:25,071] [INFO] Task started: HMMsearch
[2024-01-24 11:51:25,071] [INFO] Running command: hmmsearch --tblout GCF_000974705.1_ASM97470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/reference_markers.hmm GCF_000974705.1_ASM97470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:25,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:25,403] [INFO] Found 6/6 markers.
[2024-01-24 11:51:25,448] [INFO] Query marker FASTA was written to GCF_000974705.1_ASM97470v1_genomic.fna/markers.fasta
[2024-01-24 11:51:25,448] [INFO] Task started: Blastn
[2024-01-24 11:51:25,448] [INFO] Running command: blastn -query GCF_000974705.1_ASM97470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/reference_markers.fasta -out GCF_000974705.1_ASM97470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:26,524] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:26,528] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:26,528] [INFO] Target genome list was writen to GCF_000974705.1_ASM97470v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:26,535] [INFO] Task started: fastANI
[2024-01-24 11:51:26,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e98116-7815-4520-baad-9f805011da6c/GCF_000974705.1_ASM97470v1_genomic.fna.gz --refList GCF_000974705.1_ASM97470v1_genomic.fna/target_genomes.txt --output GCF_000974705.1_ASM97470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,894] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,894] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,904] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:37,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:37,905] [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 celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	100.0	1160	1172	95	conclusive
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	99.9716	1168	1172	95	conclusive
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	90.7805	1021	1172	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	90.7503	1023	1172	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	90.2776	1032	1172	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	90.1765	1019	1172	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	81.8077	777	1172	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	81.7703	806	1172	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	81.1858	730	1172	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	81.1634	729	1172	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	79.8954	534	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,906] [INFO] DFAST Taxonomy check result was written to GCF_000974705.1_ASM97470v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,907] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/checkm_data
[2024-01-24 11:51:37,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,954] [INFO] Task started: CheckM
[2024-01-24 11:51:37,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000974705.1_ASM97470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000974705.1_ASM97470v1_genomic.fna/checkm_input GCF_000974705.1_ASM97470v1_genomic.fna/checkm_result
[2024-01-24 11:52:18,252] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:18,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:18,274] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:18,274] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:18,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000974705.1_ASM97470v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:18,275] [INFO] Task started: Blastn
[2024-01-24 11:52:18,275] [INFO] Running command: blastn -query GCF_000974705.1_ASM97470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a82a600-04f3-44c0-b5be-9b524b26fc95/dqc_reference/reference_markers_gtdb.fasta -out GCF_000974705.1_ASM97470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:19,723] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:19,727] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:19,727] [INFO] Target genome list was writen to GCF_000974705.1_ASM97470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:19,735] [INFO] Task started: fastANI
[2024-01-24 11:52:19,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg46e98116-7815-4520-baad-9f805011da6c/GCF_000974705.1_ASM97470v1_genomic.fna.gz --refList GCF_000974705.1_ASM97470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000974705.1_ASM97470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:33,139] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:33,150] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:33,150] [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_002101595.1	s__Mycobacterium celatum	99.9716	1168	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_010728725.1	s__Mycobacterium branderi	90.7369	1024	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	90.2989	1030	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_003402475.1	s__Mycobacterium sp003402475	89.9627	1011	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672775.1	s__Mycobacterium kyorinense_A	82.9187	835	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102185.1	s__Mycobacterium fragae	82.8074	840	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731635.1	s__Mycobacterium noviomagense	81.7807	805	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	81.5781	707	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_002086635.1	s__Mycobacterium alsense	81.488	759	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	81.15	718	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667375.1	s__Mycobacterium sinense_A	80.3736	588	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_000195955.2	s__Mycobacterium tuberculosis	79.926	531	1172	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_001499905.1	s__Mycobacterium sp001499905	79.7577	530	1172	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 11:52:33,152] [INFO] GTDB search result was written to GCF_000974705.1_ASM97470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:33,152] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:33,155] [INFO] DFAST_QC result json was written to GCF_000974705.1_ASM97470v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:33,155] [INFO] DFAST_QC completed!
[2024-01-24 11:52:33,155] [INFO] Total running time: 0h1m23s