[2024-01-24 11:26:27,998] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,001] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,002] [INFO] DQC Reference Directory: /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference
[2024-01-24 11:26:29,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,379] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg786a4c0f-c149-46f4-80f8-923eb7a019e2/GCF_002086175.1_ASM208617v1_genomic.fna.gz | prodigal -d GCF_002086175.1_ASM208617v1_genomic.fna/cds.fna -a GCF_002086175.1_ASM208617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:44,732] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:44,732] [INFO] Task started: HMMsearch
[2024-01-24 11:26:44,732] [INFO] Running command: hmmsearch --tblout GCF_002086175.1_ASM208617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/reference_markers.hmm GCF_002086175.1_ASM208617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:45,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:45,045] [INFO] Found 6/6 markers.
[2024-01-24 11:26:45,097] [INFO] Query marker FASTA was written to GCF_002086175.1_ASM208617v1_genomic.fna/markers.fasta
[2024-01-24 11:26:45,098] [INFO] Task started: Blastn
[2024-01-24 11:26:45,098] [INFO] Running command: blastn -query GCF_002086175.1_ASM208617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/reference_markers.fasta -out GCF_002086175.1_ASM208617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:46,206] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:46,209] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:46,209] [INFO] Target genome list was writen to GCF_002086175.1_ASM208617v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:46,214] [INFO] Task started: fastANI
[2024-01-24 11:26:46,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg786a4c0f-c149-46f4-80f8-923eb7a019e2/GCF_002086175.1_ASM208617v1_genomic.fna.gz --refList GCF_002086175.1_ASM208617v1_genomic.fna/target_genomes.txt --output GCF_002086175.1_ASM208617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:02,523] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:02,524] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:02,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:02,536] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:02,536] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:02,536] [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=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	100.0	1598	1601	95	conclusive
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	99.9975	1601	1601	95	conclusive
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	84.8537	1227	1601	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	84.6762	1255	1601	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	84.601	1280	1601	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	84.5185	1260	1601	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	84.0872	1201	1601	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	83.0039	1088	1601	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.9609	1100	1601	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.9578	1109	1601	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	81.1917	964	1601	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	80.2733	837	1601	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.2393	841	1601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:02,541] [INFO] DFAST Taxonomy check result was written to GCF_002086175.1_ASM208617v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:02,541] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:02,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:02,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/checkm_data
[2024-01-24 11:27:02,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:02,595] [INFO] Task started: CheckM
[2024-01-24 11:27:02,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086175.1_ASM208617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086175.1_ASM208617v1_genomic.fna/checkm_input GCF_002086175.1_ASM208617v1_genomic.fna/checkm_result
[2024-01-24 11:27:49,741] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:49,743] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:49,773] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:49,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:49,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086175.1_ASM208617v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:49,774] [INFO] Task started: Blastn
[2024-01-24 11:27:49,775] [INFO] Running command: blastn -query GCF_002086175.1_ASM208617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac2d9f1e-fb29-4be0-9a3e-733a7c8129ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086175.1_ASM208617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:51,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:51,450] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:51,451] [INFO] Target genome list was writen to GCF_002086175.1_ASM208617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:51,463] [INFO] Task started: fastANI
[2024-01-24 11:27:51,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg786a4c0f-c149-46f4-80f8-923eb7a019e2/GCF_002086175.1_ASM208617v1_genomic.fna.gz --refList GCF_002086175.1_ASM208617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086175.1_ASM208617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:07,417] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:07,437] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:07,437] [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	99.9975	1601	1601	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	92.141	1400	1601	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	92.1106	1386	1601	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	85.7397	1175	1601	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	84.8554	1227	1601	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	84.7582	1269	1601	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	84.7168	1257	1601	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	84.6887	1253	1601	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	84.5421	1254	1601	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	84.5119	1261	1601	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	84.51	1299	1601	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	84.4634	1241	1601	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	82.9964	1089	1601	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 11:28:07,439] [INFO] GTDB search result was written to GCF_002086175.1_ASM208617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:07,440] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:07,444] [INFO] DFAST_QC result json was written to GCF_002086175.1_ASM208617v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:07,444] [INFO] DFAST_QC completed!
[2024-01-24 11:28:07,445] [INFO] Total running time: 0h1m39s