[2024-01-24 12:15:04,099] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference
[2024-01-24 12:15:05,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,438] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg5db1d49c-a096-4a67-9012-f049c6562e2e/GCF_010731795.1_ASM1073179v1_genomic.fna.gz | prodigal -d GCF_010731795.1_ASM1073179v1_genomic.fna/cds.fna -a GCF_010731795.1_ASM1073179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:25,618] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:25,619] [INFO] Task started: HMMsearch
[2024-01-24 12:15:25,619] [INFO] Running command: hmmsearch --tblout GCF_010731795.1_ASM1073179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/reference_markers.hmm GCF_010731795.1_ASM1073179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:25,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:25,969] [INFO] Found 6/6 markers.
[2024-01-24 12:15:26,017] [INFO] Query marker FASTA was written to GCF_010731795.1_ASM1073179v1_genomic.fna/markers.fasta
[2024-01-24 12:15:26,018] [INFO] Task started: Blastn
[2024-01-24 12:15:26,018] [INFO] Running command: blastn -query GCF_010731795.1_ASM1073179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/reference_markers.fasta -out GCF_010731795.1_ASM1073179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,111] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,115] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:27,115] [INFO] Target genome list was writen to GCF_010731795.1_ASM1073179v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:27,121] [INFO] Task started: fastANI
[2024-01-24 12:15:27,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db1d49c-a096-4a67-9012-f049c6562e2e/GCF_010731795.1_ASM1073179v1_genomic.fna.gz --refList GCF_010731795.1_ASM1073179v1_genomic.fna/target_genomes.txt --output GCF_010731795.1_ASM1073179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:42,666] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:42,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:42,685] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:42,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:42,685] [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 celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	100.0	1674	1674	95	conclusive
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	99.9585	1597	1674	95	conclusive
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	84.8203	1246	1674	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	84.6261	1282	1674	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	84.4995	1273	1674	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	84.4899	1313	1674	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	84.0759	1230	1674	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.9587	1105	1674	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.8971	1127	1674	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.8964	1134	1674	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	81.1451	986	1674	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.2681	856	1674	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.2531	845	1674	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,687] [INFO] DFAST Taxonomy check result was written to GCF_010731795.1_ASM1073179v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:42,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:42,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:42,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/checkm_data
[2024-01-24 12:15:42,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,736] [INFO] Task started: CheckM
[2024-01-24 12:15:42,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731795.1_ASM1073179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731795.1_ASM1073179v1_genomic.fna/checkm_input GCF_010731795.1_ASM1073179v1_genomic.fna/checkm_result
[2024-01-24 12:16:42,078] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:42,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:42,101] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:42,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:42,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731795.1_ASM1073179v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:42,102] [INFO] Task started: Blastn
[2024-01-24 12:16:42,102] [INFO] Running command: blastn -query GCF_010731795.1_ASM1073179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg250415f5-2cc0-4438-bcbb-d5481b5254de/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731795.1_ASM1073179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:43,718] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:43,723] [INFO] Selected 13 target genomes.
[2024-01-24 12:16:43,723] [INFO] Target genome list was writen to GCF_010731795.1_ASM1073179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:43,732] [INFO] Task started: fastANI
[2024-01-24 12:16:43,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg5db1d49c-a096-4a67-9012-f049c6562e2e/GCF_010731795.1_ASM1073179v1_genomic.fna.gz --refList GCF_010731795.1_ASM1073179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731795.1_ASM1073179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:00,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:00,617] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:00,618] [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_010731795.1	s__Mycobacterium celeriflavum	100.0	1674	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	98.14	0.96	0.92	3	conclusive
GCF_001500065.1	s__Mycobacterium sp001500065	92.1224	1404	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499855.1	s__Mycobacterium sp001499855	92.0267	1404	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.76	99.52	0.98	0.97	3	-
GCF_001672895.1	s__Mycobacterium sp001672895	85.746	1187	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	84.8159	1246	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	84.7516	1284	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001665535.1	s__Mycobacterium sp001665535	84.6664	1257	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001050035.1	s__Mycobacterium komanii	84.6245	1281	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	84.5672	1266	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	84.5074	1272	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCA_900637135.1	s__Mycobacterium flavescens	84.4924	1318	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001668575.1	s__Mycobacterium sp001668575	84.3874	1261	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	82.9822	1101	1674	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:00,619] [INFO] GTDB search result was written to GCF_010731795.1_ASM1073179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:00,620] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:00,624] [INFO] DFAST_QC result json was written to GCF_010731795.1_ASM1073179v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:00,624] [INFO] DFAST_QC completed!
[2024-01-24 12:17:00,624] [INFO] Total running time: 0h1m57s