[2024-01-24 14:05:50,043] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:50,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:50,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference
[2024-01-24 14:05:51,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:51,304] [INFO] Task started: Prodigal
[2024-01-24 14:05:51,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg30db560d-26dd-423e-8b84-24eb9da25aa1/GCF_004014795.1_Mbrumae.v1_genomic.fna.gz | prodigal -d GCF_004014795.1_Mbrumae.v1_genomic.fna/cds.fna -a GCF_004014795.1_Mbrumae.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:03,359] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:03,359] [INFO] Task started: HMMsearch
[2024-01-24 14:06:03,359] [INFO] Running command: hmmsearch --tblout GCF_004014795.1_Mbrumae.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/reference_markers.hmm GCF_004014795.1_Mbrumae.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:03,661] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:03,662] [INFO] Found 6/6 markers.
[2024-01-24 14:06:03,708] [INFO] Query marker FASTA was written to GCF_004014795.1_Mbrumae.v1_genomic.fna/markers.fasta
[2024-01-24 14:06:03,709] [INFO] Task started: Blastn
[2024-01-24 14:06:03,709] [INFO] Running command: blastn -query GCF_004014795.1_Mbrumae.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/reference_markers.fasta -out GCF_004014795.1_Mbrumae.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:05,146] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:05,156] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:05,156] [INFO] Target genome list was writen to GCF_004014795.1_Mbrumae.v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:05,165] [INFO] Task started: fastANI
[2024-01-24 14:06:05,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg30db560d-26dd-423e-8b84-24eb9da25aa1/GCF_004014795.1_Mbrumae.v1_genomic.fna.gz --refList GCF_004014795.1_Mbrumae.v1_genomic.fna/target_genomes.txt --output GCF_004014795.1_Mbrumae.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:20,874] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:20,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:20,875] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:20,885] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:20,885] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:20,886] [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
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	100.0	1265	1268	95	conclusive
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	99.996	1266	1268	95	conclusive
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	83.9176	842	1268	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	83.8841	861	1268	95	below_threshold
Mycolicibacterium insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	82.7534	825	1268	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.0128	732	1268	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.9901	739	1268	95	below_threshold
Mycobacterium palauense	strain=CECT 8779	GCA_002592005.1	2034511	2034511	type	True	80.6832	694	1268	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.1894	653	1268	95	below_threshold
Mycolicibacterium confluentis	strain=DSM 44017	GCA_002102105.1	28047	28047	type	True	80.0422	651	1268	95	below_threshold
Mycolicibacterium confluentis	strain=JCM 13671	GCA_010729895.1	28047	28047	type	True	80.014	655	1268	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	79.8447	579	1268	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	79.6678	654	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:20,887] [INFO] DFAST Taxonomy check result was written to GCF_004014795.1_Mbrumae.v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:20,888] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:20,888] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:20,888] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/checkm_data
[2024-01-24 14:06:20,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:20,930] [INFO] Task started: CheckM
[2024-01-24 14:06:20,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004014795.1_Mbrumae.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004014795.1_Mbrumae.v1_genomic.fna/checkm_input GCF_004014795.1_Mbrumae.v1_genomic.fna/checkm_result
[2024-01-24 14:07:01,462] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:01,463] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,482] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:01,482] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:01,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004014795.1_Mbrumae.v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:01,483] [INFO] Task started: Blastn
[2024-01-24 14:07:01,483] [INFO] Running command: blastn -query GCF_004014795.1_Mbrumae.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50ca3fa0-b3a2-4038-9b95-e9bd258266a8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004014795.1_Mbrumae.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:03,438] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:03,442] [INFO] Selected 19 target genomes.
[2024-01-24 14:07:03,442] [INFO] Target genome list was writen to GCF_004014795.1_Mbrumae.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:03,474] [INFO] Task started: fastANI
[2024-01-24 14:07:03,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg30db560d-26dd-423e-8b84-24eb9da25aa1/GCF_004014795.1_Mbrumae.v1_genomic.fna.gz --refList GCF_004014795.1_Mbrumae.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004014795.1_Mbrumae.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:24,730] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,751] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:24,751] [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_004014795.1	s__Mycobacterium brumae	100.0	1265	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	conclusive
GCF_010726955.1	s__Mycobacterium fallax	83.8732	862	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_010731615.1	s__Mycobacterium insubricum	82.7591	825	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900637205.1	s__Mycobacterium chitae	81.0061	733	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001583415.1	s__Mycobacterium phlei	80.8121	703	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900078775.1	s__Mycobacterium aurum_A	80.7255	687	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002592005.1	s__Mycobacterium palauense	80.6774	694	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	80.4025	661	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.2618	683	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	80.1934	653	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086115.1	s__Mycobacterium bacteremicum	80.1841	669	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667265.1	s__Mycobacterium sp001667265	80.1122	648	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329645.1	s__Mycobacterium grossiae	80.1054	667	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.93	99.93	0.94	0.94	2	-
GCF_010729895.1	s__Mycobacterium confluentis	79.9999	657	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016197405.1	s__Mycobacterium sp016197405	79.9506	655	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014805.1	s__Mycobacterium elephantis	79.8364	580	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_001457595.1	s__Mycobacterium smegmatis	79.7225	659	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002086485.1	s__Mycobacterium aquaticum	79.6541	655	1268	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	79.6165	683	1268	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 14:07:24,753] [INFO] GTDB search result was written to GCF_004014795.1_Mbrumae.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:24,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:24,758] [INFO] DFAST_QC result json was written to GCF_004014795.1_Mbrumae.v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:24,759] [INFO] DFAST_QC completed!
[2024-01-24 14:07:24,759] [INFO] Total running time: 0h1m35s