[2024-01-24 14:47:27,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:27,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:27,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference
[2024-01-24 14:47:28,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:28,629] [INFO] Task started: Prodigal
[2024-01-24 14:47:28,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg212646c3-b528-44d4-8fb5-8de53d532b9a/GCF_014323725.1_ASM1432372v1_genomic.fna.gz | prodigal -d GCF_014323725.1_ASM1432372v1_genomic.fna/cds.fna -a GCF_014323725.1_ASM1432372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:52,197] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:52,198] [INFO] Task started: HMMsearch
[2024-01-24 14:47:52,198] [INFO] Running command: hmmsearch --tblout GCF_014323725.1_ASM1432372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/reference_markers.hmm GCF_014323725.1_ASM1432372v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:52,540] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:52,541] [INFO] Found 6/6 markers.
[2024-01-24 14:47:52,599] [INFO] Query marker FASTA was written to GCF_014323725.1_ASM1432372v1_genomic.fna/markers.fasta
[2024-01-24 14:47:52,600] [INFO] Task started: Blastn
[2024-01-24 14:47:52,600] [INFO] Running command: blastn -query GCF_014323725.1_ASM1432372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/reference_markers.fasta -out GCF_014323725.1_ASM1432372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:53,936] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:53,940] [INFO] Selected 17 target genomes.
[2024-01-24 14:47:53,941] [INFO] Target genome list was writen to GCF_014323725.1_ASM1432372v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:53,956] [INFO] Task started: fastANI
[2024-01-24 14:47:53,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg212646c3-b528-44d4-8fb5-8de53d532b9a/GCF_014323725.1_ASM1432372v1_genomic.fna.gz --refList GCF_014323725.1_ASM1432372v1_genomic.fna/target_genomes.txt --output GCF_014323725.1_ASM1432372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:21,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:21,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:21,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:21,654] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:21,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:21,655] [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
Actinokineospora xionganensis	strain=HBU206404	GCA_014323725.1	2684470	2684470	type	True	100.0	2240	2242	95	conclusive
Actinokineospora alba	strain=DSM 45114	GCA_004362515.1	504798	504798	type	True	92.2037	1822	2242	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	81.9413	1102	2242	95	below_threshold
Actinokineospora spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	81.1759	1103	2242	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	81.094	1053	2242	95	below_threshold
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	81.0568	1005	2242	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.0176	1063	2242	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	80.9963	1129	2242	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	80.9707	1049	2242	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	80.9243	1050	2242	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	80.8875	1109	2242	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	80.6236	1028	2242	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	78.8376	852	2242	95	below_threshold
Actinophytocola xanthii	strain=11-183	GCA_001921205.1	1912961	1912961	type	True	78.8209	856	2242	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	78.6635	824	2242	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.4914	764	2242	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.6653	623	2242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,656] [INFO] DFAST Taxonomy check result was written to GCF_014323725.1_ASM1432372v1_genomic.fna/tc_result.tsv
[2024-01-24 14:48:21,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:21,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:21,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/checkm_data
[2024-01-24 14:48:21,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:21,726] [INFO] Task started: CheckM
[2024-01-24 14:48:21,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014323725.1_ASM1432372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014323725.1_ASM1432372v1_genomic.fna/checkm_input GCF_014323725.1_ASM1432372v1_genomic.fna/checkm_result
[2024-01-24 14:49:39,076] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:39,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:39,102] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:39,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:39,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014323725.1_ASM1432372v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:39,104] [INFO] Task started: Blastn
[2024-01-24 14:49:39,104] [INFO] Running command: blastn -query GCF_014323725.1_ASM1432372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cfb9355-9595-4024-9698-0d21c25353df/dqc_reference/reference_markers_gtdb.fasta -out GCF_014323725.1_ASM1432372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:41,162] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:41,169] [INFO] Selected 16 target genomes.
[2024-01-24 14:49:41,170] [INFO] Target genome list was writen to GCF_014323725.1_ASM1432372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:41,182] [INFO] Task started: fastANI
[2024-01-24 14:49:41,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg212646c3-b528-44d4-8fb5-8de53d532b9a/GCF_014323725.1_ASM1432372v1_genomic.fna.gz --refList GCF_014323725.1_ASM1432372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014323725.1_ASM1432372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:50:10,867] [INFO] Task succeeded: fastANI
[2024-01-24 14:50:10,881] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:50:10,881] [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_014323725.1	s__Actinokineospora xionganensis	100.0	2240	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004362515.1	s__Actinokineospora alba	92.1991	1823	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900070365.1	s__Actinokineospora sp900070365	83.6052	1361	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101685.1	s__Actinokineospora iranica	81.9301	1104	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182415.1	s__Actinokineospora mzabensis	81.2267	1130	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	-
GCF_900111175.1	s__Actinokineospora terrae	81.0847	1054	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_009745975.1	s__Actinokineospora pegani	81.0224	1011	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648415.1	s__Actinokineospora fastidiosa	81.0018	1127	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907695.1	s__Actinokineospora baliensis	80.9088	1054	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934265.1	s__Actinokineospora auranticolor	80.9003	1107	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374445.1	s__Actinokineospora enzanensis	80.6288	1027	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002815.1	s__Umezawaea tangerina	78.8414	930	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Umezawaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001921205.1	s__Actinophytocola xanthii	78.8147	856	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinophytocola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014138725.1	s__Kutzneria viridogrisea	78.563	866	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kutzneria	95.0	99.33	99.33	0.95	0.95	2	-
GCF_007713745.1	s__Amycolatopsis acidiphila	78.5559	737	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900114035.1	s__Amycolatopsis sacchari	78.3009	750	2242	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:50:10,883] [INFO] GTDB search result was written to GCF_014323725.1_ASM1432372v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:50:10,884] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:50:10,888] [INFO] DFAST_QC result json was written to GCF_014323725.1_ASM1432372v1_genomic.fna/dqc_result.json
[2024-01-24 14:50:10,888] [INFO] DFAST_QC completed!
[2024-01-24 14:50:10,888] [INFO] Total running time: 0h2m44s