[2024-01-25 19:39:50,748] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,750] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,750] [INFO] DQC Reference Directory: /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference
[2024-01-25 19:39:51,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:51,874] [INFO] Task started: Prodigal
[2024-01-25 19:39:51,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b18e5db-620d-4017-a705-00228d60afe1/GCF_001583415.1_ASM158341v1_genomic.fna.gz | prodigal -d GCF_001583415.1_ASM158341v1_genomic.fna/cds.fna -a GCF_001583415.1_ASM158341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:06,535] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:06,536] [INFO] Task started: HMMsearch
[2024-01-25 19:40:06,536] [INFO] Running command: hmmsearch --tblout GCF_001583415.1_ASM158341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/reference_markers.hmm GCF_001583415.1_ASM158341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:06,844] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:06,845] [INFO] Found 6/6 markers.
[2024-01-25 19:40:06,891] [INFO] Query marker FASTA was written to GCF_001583415.1_ASM158341v1_genomic.fna/markers.fasta
[2024-01-25 19:40:06,892] [INFO] Task started: Blastn
[2024-01-25 19:40:06,892] [INFO] Running command: blastn -query GCF_001583415.1_ASM158341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/reference_markers.fasta -out GCF_001583415.1_ASM158341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:08,233] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:08,236] [INFO] Selected 16 target genomes.
[2024-01-25 19:40:08,236] [INFO] Target genome list was writen to GCF_001583415.1_ASM158341v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:08,241] [INFO] Task started: fastANI
[2024-01-25 19:40:08,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b18e5db-620d-4017-a705-00228d60afe1/GCF_001583415.1_ASM158341v1_genomic.fna.gz --refList GCF_001583415.1_ASM158341v1_genomic.fna/target_genomes.txt --output GCF_001583415.1_ASM158341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:30,665] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:30,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:30,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:30,676] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:40:30,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:30,676] [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 phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	100.0	1782	1783	95	conclusive
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	99.9671	1749	1783	95	conclusive
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	99.9645	1742	1783	95	conclusive
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	85.0059	1355	1783	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	83.7145	1140	1783	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	83.673	1191	1783	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	83.4008	1199	1783	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	82.6822	1152	1783	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.9302	1105	1783	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.6529	1094	1783	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.9604	1058	1783	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.6246	985	1783	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.5995	956	1783	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.5597	896	1783	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.454	959	1783	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	80.2716	941	1783	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:30,677] [INFO] DFAST Taxonomy check result was written to GCF_001583415.1_ASM158341v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:30,678] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:30,678] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:30,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/checkm_data
[2024-01-25 19:40:30,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:30,728] [INFO] Task started: CheckM
[2024-01-25 19:40:30,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001583415.1_ASM158341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001583415.1_ASM158341v1_genomic.fna/checkm_input GCF_001583415.1_ASM158341v1_genomic.fna/checkm_result
[2024-01-25 19:41:33,628] [INFO] Task succeeded: CheckM
[2024-01-25 19:41:33,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:41:33,648] [INFO] ===== Completeness check finished =====
[2024-01-25 19:41:33,649] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:41:33,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001583415.1_ASM158341v1_genomic.fna/markers.fasta)
[2024-01-25 19:41:33,649] [INFO] Task started: Blastn
[2024-01-25 19:41:33,649] [INFO] Running command: blastn -query GCF_001583415.1_ASM158341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg30a58dd3-9f66-4736-a338-2fabe1db394e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001583415.1_ASM158341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:41:35,904] [INFO] Task succeeded: Blastn
[2024-01-25 19:41:35,913] [INFO] Selected 21 target genomes.
[2024-01-25 19:41:35,913] [INFO] Target genome list was writen to GCF_001583415.1_ASM158341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:41:35,923] [INFO] Task started: fastANI
[2024-01-25 19:41:35,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b18e5db-620d-4017-a705-00228d60afe1/GCF_001583415.1_ASM158341v1_genomic.fna.gz --refList GCF_001583415.1_ASM158341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001583415.1_ASM158341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:05,890] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:05,903] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:05,904] [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_001583415.1	s__Mycobacterium phlei	100.0	1783	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	conclusive
GCF_900108565.1	s__Mycobacterium rutilum	85.0008	1357	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	84.8436	1322	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900603025.1	s__Mycobacterium hassiacum	83.6737	1188	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001665535.1	s__Mycobacterium sp001665535	83.1214	1192	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001570485.1	s__Mycobacterium novocastrense	82.9351	1187	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001500025.1	s__Mycobacterium sp001500025	82.924	1181	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668575.1	s__Mycobacterium sp001668575	82.9162	1186	1783	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	82.6681	1154	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.0574	1163	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731695.1	s__Mycobacterium litorale	82.0426	1120	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	82.0297	1088	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187505.1	s__Mycobacterium goodii_B	81.9353	1106	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	81.9136	1124	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	81.7441	1108	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001457595.1	s__Mycobacterium smegmatis	81.7356	1153	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_002553505.1	s__Mycobacterium agri	81.6706	1061	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002798385.1	s__Mycobacterium goodii	81.1959	1029	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002086835.1	s__Mycobacterium porcinum	80.8266	1056	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.7733	989	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729895.1	s__Mycobacterium confluentis	80.5541	979	1783	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:05,905] [INFO] GTDB search result was written to GCF_001583415.1_ASM158341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:05,905] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:05,909] [INFO] DFAST_QC result json was written to GCF_001583415.1_ASM158341v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:05,910] [INFO] DFAST_QC completed!
[2024-01-25 19:42:05,910] [INFO] Total running time: 0h2m15s