[2024-01-24 11:05:22,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:22,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:22,669] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference
[2024-01-24 11:05:23,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:23,898] [INFO] Task started: Prodigal
[2024-01-24 11:05:23,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgb45c4ada-d719-4746-8459-453155011a66/GCF_025823075.1_ASM2582307v1_genomic.fna.gz | prodigal -d GCF_025823075.1_ASM2582307v1_genomic.fna/cds.fna -a GCF_025823075.1_ASM2582307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:45,496] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:45,496] [INFO] Task started: HMMsearch
[2024-01-24 11:05:45,496] [INFO] Running command: hmmsearch --tblout GCF_025823075.1_ASM2582307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/reference_markers.hmm GCF_025823075.1_ASM2582307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:45,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:45,854] [INFO] Found 6/6 markers.
[2024-01-24 11:05:45,915] [INFO] Query marker FASTA was written to GCF_025823075.1_ASM2582307v1_genomic.fna/markers.fasta
[2024-01-24 11:05:45,915] [INFO] Task started: Blastn
[2024-01-24 11:05:45,915] [INFO] Running command: blastn -query GCF_025823075.1_ASM2582307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/reference_markers.fasta -out GCF_025823075.1_ASM2582307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:47,246] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:47,250] [INFO] Selected 14 target genomes.
[2024-01-24 11:05:47,251] [INFO] Target genome list was writen to GCF_025823075.1_ASM2582307v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:47,260] [INFO] Task started: fastANI
[2024-01-24 11:05:47,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45c4ada-d719-4746-8459-453155011a66/GCF_025823075.1_ASM2582307v1_genomic.fna.gz --refList GCF_025823075.1_ASM2582307v1_genomic.fna/target_genomes.txt --output GCF_025823075.1_ASM2582307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:05,732] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:05,733] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:05,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:05,747] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:05,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:05,747] [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 fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	99.9916	2108	2121	95	conclusive
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	85.0337	1418	2121	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	85.0035	1422	2121	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	84.9097	1468	2121	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	84.8697	1479	2121	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	81.4085	1129	2121	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.4721	959	2121	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.3867	758	2121	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.3501	779	2121	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.1693	932	2121	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.9606	967	2121	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	79.864	932	2121	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6092	868	2121	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.1852	850	2121	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:05,749] [INFO] DFAST Taxonomy check result was written to GCF_025823075.1_ASM2582307v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:05,750] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:05,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:05,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/checkm_data
[2024-01-24 11:06:05,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:05,815] [INFO] Task started: CheckM
[2024-01-24 11:06:05,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823075.1_ASM2582307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823075.1_ASM2582307v1_genomic.fna/checkm_input GCF_025823075.1_ASM2582307v1_genomic.fna/checkm_result
[2024-01-24 11:07:12,861] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:12,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:12,886] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:12,886] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:12,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823075.1_ASM2582307v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:12,887] [INFO] Task started: Blastn
[2024-01-24 11:07:12,887] [INFO] Running command: blastn -query GCF_025823075.1_ASM2582307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd294968-f40d-461d-85e8-fe4dcf2fee11/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823075.1_ASM2582307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:14,913] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:14,917] [INFO] Selected 17 target genomes.
[2024-01-24 11:07:14,917] [INFO] Target genome list was writen to GCF_025823075.1_ASM2582307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:14,928] [INFO] Task started: fastANI
[2024-01-24 11:07:14,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgb45c4ada-d719-4746-8459-453155011a66/GCF_025823075.1_ASM2582307v1_genomic.fna.gz --refList GCF_025823075.1_ASM2582307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823075.1_ASM2582307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:37,321] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:37,343] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:37,343] [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_011758805.1	s__Mycobacterium fluoranthenivorans	99.9916	2108	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	conclusive
GCA_016197365.1	s__Mycobacterium cosmeticum_A	85.867	1339	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101555.1	s__Mycobacterium canariasense	85.0201	1420	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000613185.1	s__Mycobacterium cosmeticum	84.8769	1478	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	81.9332	1149	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_900078775.1	s__Mycobacterium aurum_A	81.8558	1174	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	81.7493	1160	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_008329585.1	s__Mycobacterium sp008329585	81.6727	1161	2121	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	81.5434	1116	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_002086115.1	s__Mycobacterium bacteremicum	81.4021	1130	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	80.8378	1016	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_017876775.1	s__Mycobacterium lutetiense	80.6677	956	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726955.1	s__Mycobacterium fallax	80.3569	777	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_004762045.1	s__Mycobacterium sp004762045	80.3081	1012	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102345.1	s__Mycobacterium peregrinum	80.2244	975	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	-
GCF_000612725.1	s__Mycobacterium austroafricanum	79.9408	969	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002798385.1	s__Mycobacterium goodii	79.7184	947	2121	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:37,345] [INFO] GTDB search result was written to GCF_025823075.1_ASM2582307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:37,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:37,350] [INFO] DFAST_QC result json was written to GCF_025823075.1_ASM2582307v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:37,350] [INFO] DFAST_QC completed!
[2024-01-24 11:07:37,350] [INFO] Total running time: 0h2m15s