[2024-01-24 12:39:41,874] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,876] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,876] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference
[2024-01-24 12:39:43,223] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,224] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,225] [INFO] Running command: gunzip -c /var/lib/cwl/stg6694624a-d210-49a5-bae2-8930c349884e/GCF_900187065.1_50465_H02_genomic.fna.gz | prodigal -d GCF_900187065.1_50465_H02_genomic.fna/cds.fna -a GCF_900187065.1_50465_H02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:00,099] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:00,099] [INFO] Task started: HMMsearch
[2024-01-24 12:40:00,099] [INFO] Running command: hmmsearch --tblout GCF_900187065.1_50465_H02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/reference_markers.hmm GCF_900187065.1_50465_H02_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:00,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:00,442] [INFO] Found 6/6 markers.
[2024-01-24 12:40:00,502] [INFO] Query marker FASTA was written to GCF_900187065.1_50465_H02_genomic.fna/markers.fasta
[2024-01-24 12:40:00,502] [INFO] Task started: Blastn
[2024-01-24 12:40:00,503] [INFO] Running command: blastn -query GCF_900187065.1_50465_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/reference_markers.fasta -out GCF_900187065.1_50465_H02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:01,730] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:01,733] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:01,734] [INFO] Target genome list was writen to GCF_900187065.1_50465_H02_genomic.fna/target_genomes.txt
[2024-01-24 12:40:01,740] [INFO] Task started: fastANI
[2024-01-24 12:40:01,740] [INFO] Running command: fastANI --query /var/lib/cwl/stg6694624a-d210-49a5-bae2-8930c349884e/GCF_900187065.1_50465_H02_genomic.fna.gz --refList GCF_900187065.1_50465_H02_genomic.fna/target_genomes.txt --output GCF_900187065.1_50465_H02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:18,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:18,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:18,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:18,118] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:40:18,118] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:18,118] [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 thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	100.0	1649	1650	95	conclusive
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	99.9644	1592	1650	95	conclusive
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	99.9355	1591	1650	95	conclusive
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	81.9275	1014	1650	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	81.8985	964	1650	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.8656	1007	1650	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.8344	1029	1650	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.9824	947	1650	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.689	938	1650	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.5826	960	1650	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	80.1253	837	1650	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	79.9015	718	1650	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	79.8534	582	1650	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.4266	775	1650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:18,120] [INFO] DFAST Taxonomy check result was written to GCF_900187065.1_50465_H02_genomic.fna/tc_result.tsv
[2024-01-24 12:40:18,121] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:18,121] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:18,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/checkm_data
[2024-01-24 12:40:18,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:18,172] [INFO] Task started: CheckM
[2024-01-24 12:40:18,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900187065.1_50465_H02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900187065.1_50465_H02_genomic.fna/checkm_input GCF_900187065.1_50465_H02_genomic.fna/checkm_result
[2024-01-24 12:41:41,522] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:41,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:41,551] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:41,552] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:41,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900187065.1_50465_H02_genomic.fna/markers.fasta)
[2024-01-24 12:41:41,552] [INFO] Task started: Blastn
[2024-01-24 12:41:41,553] [INFO] Running command: blastn -query GCF_900187065.1_50465_H02_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5e32637-61ab-42bc-9e7c-4c9351a66c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900187065.1_50465_H02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:43,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:43,245] [INFO] Selected 22 target genomes.
[2024-01-24 12:41:43,245] [INFO] Target genome list was writen to GCF_900187065.1_50465_H02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:43,256] [INFO] Task started: fastANI
[2024-01-24 12:41:43,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg6694624a-d210-49a5-bae2-8930c349884e/GCF_900187065.1_50465_H02_genomic.fna.gz --refList GCF_900187065.1_50465_H02_genomic.fna/target_genomes_gtdb.txt --output GCF_900187065.1_50465_H02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:42:10,112] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:10,134] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:42:10,134] [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_900187065.1	s__Mycobacterium thermoresistibile	100.0	1650	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_900603025.1	s__Mycobacterium hassiacum	82.0893	1028	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001583415.1	s__Mycobacterium phlei	81.8327	1027	1650	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	81.1455	942	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	81.1257	914	1650	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	81.0197	910	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731695.1	s__Mycobacterium litorale	80.9442	923	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900108565.1	s__Mycobacterium rutilum	80.9403	952	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725725.1	s__Mycobacterium pulveris	80.705	934	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722355.1	s__Mycobacterium holsaticum	80.5741	858	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665575.1	s__Mycobacterium sp001665575	80.2353	794	1650	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	80.2311	906	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCA_900637135.1	s__Mycobacterium flavescens	80.2232	856	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001665535.1	s__Mycobacterium sp001665535	80.1933	882	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001457595.1	s__Mycobacterium smegmatis	80.1738	928	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_900240945.1	s__Mycobacterium sp900240945	80.0769	867	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	80.0179	835	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_001667505.1	s__Mycobacterium sp001667505	79.9416	808	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017312405.1	s__Mycobacterium sp017312405	79.9031	813	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	79.8957	738	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002101595.1	s__Mycobacterium celatum	79.8946	720	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010731635.1	s__Mycobacterium noviomagense	78.9961	638	1650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:42:10,136] [INFO] GTDB search result was written to GCF_900187065.1_50465_H02_genomic.fna/result_gtdb.tsv
[2024-01-24 12:42:10,137] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:42:10,142] [INFO] DFAST_QC result json was written to GCF_900187065.1_50465_H02_genomic.fna/dqc_result.json
[2024-01-24 12:42:10,142] [INFO] DFAST_QC completed!
[2024-01-24 12:42:10,143] [INFO] Total running time: 0h2m28s