[2024-01-25 18:11:35,768] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,771] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,771] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference
[2024-01-25 18:11:36,909] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,909] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg90be4111-bb51-478e-bf7b-e5ce720ac90b/GCF_002102015.1_ASM210201v1_genomic.fna.gz | prodigal -d GCF_002102015.1_ASM210201v1_genomic.fna/cds.fna -a GCF_002102015.1_ASM210201v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:50,816] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:50,817] [INFO] Task started: HMMsearch
[2024-01-25 18:11:50,817] [INFO] Running command: hmmsearch --tblout GCF_002102015.1_ASM210201v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/reference_markers.hmm GCF_002102015.1_ASM210201v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:51,133] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:51,134] [INFO] Found 6/6 markers.
[2024-01-25 18:11:51,174] [INFO] Query marker FASTA was written to GCF_002102015.1_ASM210201v1_genomic.fna/markers.fasta
[2024-01-25 18:11:51,174] [INFO] Task started: Blastn
[2024-01-25 18:11:51,175] [INFO] Running command: blastn -query GCF_002102015.1_ASM210201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/reference_markers.fasta -out GCF_002102015.1_ASM210201v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:52,181] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:52,184] [INFO] Selected 12 target genomes.
[2024-01-25 18:11:52,184] [INFO] Target genome list was writen to GCF_002102015.1_ASM210201v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:52,197] [INFO] Task started: fastANI
[2024-01-25 18:11:52,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg90be4111-bb51-478e-bf7b-e5ce720ac90b/GCF_002102015.1_ASM210201v1_genomic.fna.gz --refList GCF_002102015.1_ASM210201v1_genomic.fna/target_genomes.txt --output GCF_002102015.1_ASM210201v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:06,804] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:06,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:06,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:06,813] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:12:06,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:06,813] [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 xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	100.0	1557	1570	95	conclusive
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	99.9906	1555	1570	95	conclusive
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	99.9664	1514	1570	95	conclusive
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	90.4009	1276	1570	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	84.3358	1088	1570	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.0209	817	1570	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	79.945	776	1570	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	79.908	769	1570	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	79.7123	776	1570	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	79.5888	766	1570	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	79.5683	774	1570	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	78.2895	604	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:06,815] [INFO] DFAST Taxonomy check result was written to GCF_002102015.1_ASM210201v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:06,815] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:06,815] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:06,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/checkm_data
[2024-01-25 18:12:06,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:06,863] [INFO] Task started: CheckM
[2024-01-25 18:12:06,863] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102015.1_ASM210201v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102015.1_ASM210201v1_genomic.fna/checkm_input GCF_002102015.1_ASM210201v1_genomic.fna/checkm_result
[2024-01-25 18:12:46,718] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:46,719] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:46,739] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:46,739] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:46,740] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102015.1_ASM210201v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:46,740] [INFO] Task started: Blastn
[2024-01-25 18:12:46,740] [INFO] Running command: blastn -query GCF_002102015.1_ASM210201v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3b5568f-dd07-4fd6-b33a-8e715f4a2930/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102015.1_ASM210201v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:48,176] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:48,180] [INFO] Selected 21 target genomes.
[2024-01-25 18:12:48,181] [INFO] Target genome list was writen to GCF_002102015.1_ASM210201v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:48,208] [INFO] Task started: fastANI
[2024-01-25 18:12:48,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg90be4111-bb51-478e-bf7b-e5ce720ac90b/GCF_002102015.1_ASM210201v1_genomic.fna.gz --refList GCF_002102015.1_ASM210201v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102015.1_ASM210201v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:12,732] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:12,745] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:12,745] [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_009936235.1	s__Mycobacterium xenopi	99.9664	1514	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.67	99.09	0.97	0.94	5	conclusive
GCF_016592155.1	s__Mycobacterium heckeshornense	90.3911	1276	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_010731635.1	s__Mycobacterium noviomagense	84.2887	1129	1570	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	81.7443	986	1570	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	81.5767	971	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003402475.1	s__Mycobacterium sp003402475	81.536	977	1570	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	80.7952	951	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	80.4744	850	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_002101785.1	s__Mycobacterium palustre	80.4686	856	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668725.1	s__Mycobacterium sp001668725	80.3223	846	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCA_002101905.1	s__Mycobacterium shimoidei	80.2822	830	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.0529	780	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_001665295.1	s__Mycobacterium sp001665295	80.0286	857	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.0076	798	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954275.1	s__Mycobacterium sp001954275	79.9856	838	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_010731535.1	s__Mycobacterium lacus	79.9155	780	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000689255.1	s__Mycobacterium triplex	79.8359	833	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002086125.1	s__Mycobacterium arosiense	79.7151	775	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236925.1	s__Mycobacterium sp019236925	79.5868	724	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	78.4731	634	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	78.291	604	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:12,747] [INFO] GTDB search result was written to GCF_002102015.1_ASM210201v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:12,747] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:12,751] [INFO] DFAST_QC result json was written to GCF_002102015.1_ASM210201v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:12,751] [INFO] DFAST_QC completed!
[2024-01-25 18:13:12,751] [INFO] Total running time: 0h1m37s