[2024-01-24 12:14:33,690] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference
[2024-01-24 12:14:34,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,990] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1587d7e-ca0d-4795-9aa1-5db5b37ed92a/GCF_000564855.1_ActEG49_genomic.fna.gz | prodigal -d GCF_000564855.1_ActEG49_genomic.fna/cds.fna -a GCF_000564855.1_ActEG49_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:03,190] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:03,190] [INFO] Task started: HMMsearch
[2024-01-24 12:15:03,191] [INFO] Running command: hmmsearch --tblout GCF_000564855.1_ActEG49_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/reference_markers.hmm GCF_000564855.1_ActEG49_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:03,494] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:03,495] [INFO] Found 6/6 markers.
[2024-01-24 12:15:03,550] [INFO] Query marker FASTA was written to GCF_000564855.1_ActEG49_genomic.fna/markers.fasta
[2024-01-24 12:15:03,551] [INFO] Task started: Blastn
[2024-01-24 12:15:03,551] [INFO] Running command: blastn -query GCF_000564855.1_ActEG49_genomic.fna/markers.fasta -db /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/reference_markers.fasta -out GCF_000564855.1_ActEG49_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,831] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,834] [INFO] Selected 18 target genomes.
[2024-01-24 12:15:04,834] [INFO] Target genome list was writen to GCF_000564855.1_ActEG49_genomic.fna/target_genomes.txt
[2024-01-24 12:15:04,839] [INFO] Task started: fastANI
[2024-01-24 12:15:04,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1587d7e-ca0d-4795-9aa1-5db5b37ed92a/GCF_000564855.1_ActEG49_genomic.fna.gz --refList GCF_000564855.1_ActEG49_genomic.fna/target_genomes.txt --output GCF_000564855.1_ActEG49_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:38,219] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:38,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:38,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:38,230] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:38,231] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:38,231] [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 spheciospongiae	strain=EG49	GCA_000564855.1	909613	909613	type	True	100.0	2363	2383	95	conclusive
Actinokineospora pegani	strain=TRM 65233	GCA_009745975.1	2654637	2654637	type	True	84.4952	1446	2383	95	below_threshold
Actinokineospora bangkokensis	strain=44EHW	GCA_001940455.1	1193682	1193682	type	True	84.1413	1500	2383	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	82.1683	1227	2383	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	81.8326	1201	2383	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	81.7021	1229	2383	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	81.6637	1188	2383	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	81.5783	1168	2383	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	81.4846	1182	2383	95	below_threshold
Actinokineospora auranticolor	strain=YU 961-1	GCA_002934265.1	155976	155976	type	True	81.4172	1255	2383	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	81.4018	1148	2383	95	below_threshold
Actinokineospora inagensis	strain=DSM 44258	GCA_000482865.1	103730	103730	type	True	81.3152	1091	2383	95	below_threshold
Actinokineospora fastidiosa	strain=JCM 3276	GCA_014648415.1	1816	1816	type	True	81.1229	1183	2383	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	78.4805	856	2383	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	78.4428	863	2383	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.2923	862	2383	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.0648	847	2383	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.0584	1009	2383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:38,233] [INFO] DFAST Taxonomy check result was written to GCF_000564855.1_ActEG49_genomic.fna/tc_result.tsv
[2024-01-24 12:15:38,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:38,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:38,234] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/checkm_data
[2024-01-24 12:15:38,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:38,301] [INFO] Task started: CheckM
[2024-01-24 12:15:38,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000564855.1_ActEG49_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000564855.1_ActEG49_genomic.fna/checkm_input GCF_000564855.1_ActEG49_genomic.fna/checkm_result
[2024-01-24 12:17:59,810] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:59,811] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:59,830] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:59,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:59,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000564855.1_ActEG49_genomic.fna/markers.fasta)
[2024-01-24 12:17:59,830] [INFO] Task started: Blastn
[2024-01-24 12:17:59,830] [INFO] Running command: blastn -query GCF_000564855.1_ActEG49_genomic.fna/markers.fasta -db /var/lib/cwl/stg075db725-4e61-4c6e-b132-53fca74979a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000564855.1_ActEG49_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:01,776] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:01,779] [INFO] Selected 12 target genomes.
[2024-01-24 12:18:01,779] [INFO] Target genome list was writen to GCF_000564855.1_ActEG49_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:01,784] [INFO] Task started: fastANI
[2024-01-24 12:18:01,785] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1587d7e-ca0d-4795-9aa1-5db5b37ed92a/GCF_000564855.1_ActEG49_genomic.fna.gz --refList GCF_000564855.1_ActEG49_genomic.fna/target_genomes_gtdb.txt --output GCF_000564855.1_ActEG49_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:18:24,527] [INFO] Task succeeded: fastANI
[2024-01-24 12:18:24,535] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:18:24,536] [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_003182415.1	s__Actinokineospora mzabensis	98.9619	2273	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	98.96	98.96	0.95	0.95	2	conclusive
GCF_009745975.1	s__Actinokineospora pegani	84.5484	1439	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940455.1	s__Actinokineospora bangkokensis	84.2235	1487	2383	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	82.1537	1230	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	81.8508	1199	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCF_016907695.1	s__Actinokineospora baliensis	81.4945	1182	2383	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	81.4292	1252	2383	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	81.3876	1151	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482865.1	s__Actinokineospora inagensis	81.2473	1102	2383	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	81.1229	1185	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405885.1	s__Gandjariella thermophila	78.6671	818	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Gandjariella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	78.4425	863	2383	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:18:24,537] [INFO] GTDB search result was written to GCF_000564855.1_ActEG49_genomic.fna/result_gtdb.tsv
[2024-01-24 12:18:24,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:18:24,541] [INFO] DFAST_QC result json was written to GCF_000564855.1_ActEG49_genomic.fna/dqc_result.json
[2024-01-24 12:18:24,541] [INFO] DFAST_QC completed!
[2024-01-24 12:18:24,541] [INFO] Total running time: 0h3m51s