[2024-01-24 11:59:13,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:13,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:13,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference
[2024-01-24 11:59:14,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,356] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,356] [INFO] Running command: gunzip -c /var/lib/cwl/stg27cf8826-2cec-4e65-8414-97ea3cf6e7ab/GCF_019645835.1_ASM1964583v1_genomic.fna.gz | prodigal -d GCF_019645835.1_ASM1964583v1_genomic.fna/cds.fna -a GCF_019645835.1_ASM1964583v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:42,919] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:42,920] [INFO] Task started: HMMsearch
[2024-01-24 11:59:42,920] [INFO] Running command: hmmsearch --tblout GCF_019645835.1_ASM1964583v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/reference_markers.hmm GCF_019645835.1_ASM1964583v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:43,264] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:43,265] [INFO] Found 6/6 markers.
[2024-01-24 11:59:43,313] [INFO] Query marker FASTA was written to GCF_019645835.1_ASM1964583v1_genomic.fna/markers.fasta
[2024-01-24 11:59:43,314] [INFO] Task started: Blastn
[2024-01-24 11:59:43,314] [INFO] Running command: blastn -query GCF_019645835.1_ASM1964583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/reference_markers.fasta -out GCF_019645835.1_ASM1964583v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:44,457] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:44,461] [INFO] Selected 26 target genomes.
[2024-01-24 11:59:44,461] [INFO] Target genome list was writen to GCF_019645835.1_ASM1964583v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:44,470] [INFO] Task started: fastANI
[2024-01-24 11:59:44,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cf8826-2cec-4e65-8414-97ea3cf6e7ab/GCF_019645835.1_ASM1964583v1_genomic.fna.gz --refList GCF_019645835.1_ASM1964583v1_genomic.fna/target_genomes.txt --output GCF_019645835.1_ASM1964583v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:15,636] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:15,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:15,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:15,664] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:15,664] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:15,665] [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 elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	87.1648	1428	1874	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	87.017	1440	1874	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	82.7175	1177	1874	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.6221	1123	1874	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.6049	1142	1874	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.5885	1127	1874	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	82.3212	1182	1874	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	82.0877	1181	1874	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	82.0776	1173	1874	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	81.4272	1065	1874	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	81.3574	1035	1874	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.8675	980	1874	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.6819	959	1874	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.6338	958	1874	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.1359	929	1874	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.0853	958	1874	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	80.0193	798	1874	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	79.9975	774	1874	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	79.9574	893	1874	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	79.9052	777	1874	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8849	847	1874	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	79.8836	625	1874	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.8022	918	1874	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.758	864	1874	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.6502	742	1874	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	78.3313	543	1874	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:15,667] [INFO] DFAST Taxonomy check result was written to GCF_019645835.1_ASM1964583v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:15,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:15,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:15,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/checkm_data
[2024-01-24 12:00:15,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:15,723] [INFO] Task started: CheckM
[2024-01-24 12:00:15,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019645835.1_ASM1964583v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019645835.1_ASM1964583v1_genomic.fna/checkm_input GCF_019645835.1_ASM1964583v1_genomic.fna/checkm_result
[2024-01-24 12:01:35,164] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:35,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:35,189] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:35,190] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:35,190] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019645835.1_ASM1964583v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:35,190] [INFO] Task started: Blastn
[2024-01-24 12:01:35,191] [INFO] Running command: blastn -query GCF_019645835.1_ASM1964583v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20b66a90-48af-4ea5-95b7-b6dae1071532/dqc_reference/reference_markers_gtdb.fasta -out GCF_019645835.1_ASM1964583v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:36,778] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:36,782] [INFO] Selected 24 target genomes.
[2024-01-24 12:01:36,783] [INFO] Target genome list was writen to GCF_019645835.1_ASM1964583v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:36,817] [INFO] Task started: fastANI
[2024-01-24 12:01:36,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cf8826-2cec-4e65-8414-97ea3cf6e7ab/GCF_019645835.1_ASM1964583v1_genomic.fna.gz --refList GCF_019645835.1_ASM1964583v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019645835.1_ASM1964583v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:05,975] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:06,006] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:06,006] [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_001722355.1	s__Mycobacterium holsaticum	98.7928	1536	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004014805.1	s__Mycobacterium elephantis	87.1781	1426	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_010725725.1	s__Mycobacterium pulveris	87.0145	1441	1874	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	82.7158	1174	1874	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	82.602	1142	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001722335.1	s__Mycobacterium flavescens_A	82.5429	1216	1874	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	82.3313	1181	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	82.142	1199	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001570485.1	s__Mycobacterium novocastrense	82.0221	1200	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_003284965.1	s__Mycobacterium sp003284965	81.8922	1094	1874	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	81.8045	1164	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499905.1	s__Mycobacterium sp001499905	81.728	1098	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240945.1	s__Mycobacterium sp900240945	81.2484	1109	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	81.0571	1074	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	80.7733	1059	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_000266905.1	s__Mycobacterium chubuense_A	80.7337	991	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	80.3816	938	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	80.1485	951	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_002101735.1	s__Mycobacterium kyorinense	80.0156	799	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002086485.1	s__Mycobacterium aquaticum	79.9504	894	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101595.1	s__Mycobacterium celatum	79.9025	778	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007714205.1	s__Mycobacterium helveticum	79.6422	741	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	79.4878	747	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_000195955.2	s__Mycobacterium tuberculosis	78.3246	544	1874	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:06,008] [INFO] GTDB search result was written to GCF_019645835.1_ASM1964583v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:06,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:06,013] [INFO] DFAST_QC result json was written to GCF_019645835.1_ASM1964583v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:06,013] [INFO] DFAST_QC completed!
[2024-01-24 12:02:06,013] [INFO] Total running time: 0h2m53s