[2024-01-25 19:07:05,690] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:05,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:05,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference
[2024-01-25 19:07:06,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:06,875] [INFO] Task started: Prodigal
[2024-01-25 19:07:06,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c3a8f25-cd5e-4385-bd06-9fcfc0c12881/GCF_025821585.1_ASM2582158v1_genomic.fna.gz | prodigal -d GCF_025821585.1_ASM2582158v1_genomic.fna/cds.fna -a GCF_025821585.1_ASM2582158v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:24,110] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:24,111] [INFO] Task started: HMMsearch
[2024-01-25 19:07:24,111] [INFO] Running command: hmmsearch --tblout GCF_025821585.1_ASM2582158v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/reference_markers.hmm GCF_025821585.1_ASM2582158v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:24,394] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:24,395] [INFO] Found 6/6 markers.
[2024-01-25 19:07:24,449] [INFO] Query marker FASTA was written to GCF_025821585.1_ASM2582158v1_genomic.fna/markers.fasta
[2024-01-25 19:07:24,449] [INFO] Task started: Blastn
[2024-01-25 19:07:24,449] [INFO] Running command: blastn -query GCF_025821585.1_ASM2582158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/reference_markers.fasta -out GCF_025821585.1_ASM2582158v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:25,557] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:25,560] [INFO] Selected 23 target genomes.
[2024-01-25 19:07:25,560] [INFO] Target genome list was writen to GCF_025821585.1_ASM2582158v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:25,571] [INFO] Task started: fastANI
[2024-01-25 19:07:25,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3a8f25-cd5e-4385-bd06-9fcfc0c12881/GCF_025821585.1_ASM2582158v1_genomic.fna.gz --refList GCF_025821585.1_ASM2582158v1_genomic.fna/target_genomes.txt --output GCF_025821585.1_ASM2582158v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:53,681] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:53,681] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:53,682] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:53,695] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:07:53,695] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:07:53,695] [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 chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	82.1634	1195	2013	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	82.1559	1209	2013	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	82.081	1187	2013	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	82.0164	1150	2013	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	81.9674	1096	2013	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	81.8913	1208	2013	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.6722	1257	2013	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.6551	1238	2013	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.9019	1045	2013	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.8889	1052	2013	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.8731	1055	2013	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.7823	1065	2013	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	80.2921	934	2013	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.2104	953	2013	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.1627	978	2013	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	80.1172	953	2013	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.9926	1014	2013	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	79.8989	944	2013	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	79.8154	995	2013	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.5601	918	2013	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.5297	783	2013	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3941	861	2013	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.0955	698	2013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:53,697] [INFO] DFAST Taxonomy check result was written to GCF_025821585.1_ASM2582158v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:53,697] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:53,697] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:53,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/checkm_data
[2024-01-25 19:07:53,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:53,754] [INFO] Task started: CheckM
[2024-01-25 19:07:53,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821585.1_ASM2582158v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821585.1_ASM2582158v1_genomic.fna/checkm_input GCF_025821585.1_ASM2582158v1_genomic.fna/checkm_result
[2024-01-25 19:09:01,755] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:01,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:01,782] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:01,782] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:01,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821585.1_ASM2582158v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:01,784] [INFO] Task started: Blastn
[2024-01-25 19:09:01,784] [INFO] Running command: blastn -query GCF_025821585.1_ASM2582158v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17703cbb-7990-4136-9a7c-bea9274b2e28/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821585.1_ASM2582158v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:03,378] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:03,385] [INFO] Selected 20 target genomes.
[2024-01-25 19:09:03,386] [INFO] Target genome list was writen to GCF_025821585.1_ASM2582158v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:03,407] [INFO] Task started: fastANI
[2024-01-25 19:09:03,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c3a8f25-cd5e-4385-bd06-9fcfc0c12881/GCF_025821585.1_ASM2582158v1_genomic.fna.gz --refList GCF_025821585.1_ASM2582158v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821585.1_ASM2582158v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:32,500] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:32,512] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:32,513] [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_010723735.1	s__Mycobacterium hippocampi_B	99.9948	2010	2013	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_902705885.1	s__Mycobacterium vanbaalenii_A	89.9395	1626	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013390125.1	s__Mycobacterium hippocampi_A	84.2514	1429	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222675.1	s__Mycobacterium sp005222675	83.0671	1350	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	82.1199	1293	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.1164	1033	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	82.0136	1149	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_000266905.1	s__Mycobacterium chubuense_A	82.0087	1190	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552715.1	s__Mycobacterium vaccae	81.9688	1095	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.97	1.00	1.00	3	-
GCF_900637195.1	s__Mycobacterium aurum	81.6777	1256	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001044245.1	s__Mycobacterium obuense	81.4032	1028	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_001583415.1	s__Mycobacterium phlei	80.8472	1059	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_004014805.1	s__Mycobacterium elephantis	80.1782	960	2013	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	80.1589	980	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620625.1	s__Mycobacterium sp000620625	79.9273	985	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729665.1	s__Mycobacterium madagascariense	79.6864	853	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197405.1	s__Mycobacterium sp016197405	79.6565	856	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426545.1	s__Mycobacterium sp001426545	79.5091	853	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	79.3487	877	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCF_002086635.1	s__Mycobacterium alsense	79.0419	769	2013	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:32,514] [INFO] GTDB search result was written to GCF_025821585.1_ASM2582158v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:32,515] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:32,519] [INFO] DFAST_QC result json was written to GCF_025821585.1_ASM2582158v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:32,519] [INFO] DFAST_QC completed!
[2024-01-25 19:09:32,519] [INFO] Total running time: 0h2m27s