[2023-03-16 08:41:09,467] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:41:09,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:41:09,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference
[2023-03-16 08:41:10,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:41:10,536] [INFO] Task started: Prodigal
[2023-03-16 08:41:10,536] [INFO] Running command: cat /var/lib/cwl/stgc2691788-d987-4e5f-8789-6d18eb8cd9aa/OceanDNA-b3199.fa | prodigal -d OceanDNA-b3199/cds.fna -a OceanDNA-b3199/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:41:22,144] [INFO] Task succeeded: Prodigal
[2023-03-16 08:41:22,144] [INFO] Task started: HMMsearch
[2023-03-16 08:41:22,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b3199/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/reference_markers.hmm OceanDNA-b3199/protein.faa > /dev/null
[2023-03-16 08:41:22,325] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:41:22,325] [INFO] Found 6/6 markers.
[2023-03-16 08:41:22,356] [INFO] Query marker FASTA was written to OceanDNA-b3199/markers.fasta
[2023-03-16 08:41:22,357] [INFO] Task started: Blastn
[2023-03-16 08:41:22,357] [INFO] Running command: blastn -query OceanDNA-b3199/markers.fasta -db /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/reference_markers.fasta -out OceanDNA-b3199/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:41:23,215] [INFO] Task succeeded: Blastn
[2023-03-16 08:41:23,219] [INFO] Selected 37 target genomes.
[2023-03-16 08:41:23,219] [INFO] Target genome list was writen to OceanDNA-b3199/target_genomes.txt
[2023-03-16 08:41:23,237] [INFO] Task started: fastANI
[2023-03-16 08:41:23,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2691788-d987-4e5f-8789-6d18eb8cd9aa/OceanDNA-b3199.fa --refList OceanDNA-b3199/target_genomes.txt --output OceanDNA-b3199/fastani_result.tsv --threads 1
[2023-03-16 08:41:55,618] [INFO] Task succeeded: fastANI
[2023-03-16 08:41:55,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:41:55,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:41:55,636] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:41:55,636] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:41:55,636] [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
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	76.9555	77	605	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	76.7487	89	605	95	below_threshold
Sporichthya polymorpha	strain=DSM 43042	GCA_000384115.1	35751	35751	type	True	76.6323	93	605	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	76.4696	91	605	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	76.4398	85	605	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	76.3104	69	605	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	76.3015	83	605	95	below_threshold
Streptomyces echinatus	strain=JCM4574	GCA_020400685.1	67293	67293	type	True	76.2906	80	605	95	below_threshold
Streptomyces echinatus	strain=CECT 3313	GCA_014203595.1	67293	67293	type	True	76.2867	83	605	95	below_threshold
Streptomyces pinistramenti	strain=SF28	GCA_020564935.1	2884812	2884812	type	True	76.2852	77	605	95	below_threshold
Streptomyces broussonetiae	strain=T44	GCA_009796285.1	2686304	2686304	type	True	76.2655	95	605	95	below_threshold
Actinokineospora baliensis	strain=DSM 45656	GCA_016907695.1	547056	547056	type	True	76.256	81	605	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	76.2182	97	605	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	76.1722	82	605	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	76.1535	88	605	95	below_threshold
Nocardia takedensis	strain=NBRC 100417	GCA_000308695.1	259390	259390	type	True	76.1512	63	605	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.1465	83	605	95	below_threshold
Streptomyces chattanoogensis	strain=NRRL ISP-5002	GCA_001294335.1	66876	66876	type	True	76.1387	86	605	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	76.1325	66	605	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	76.1011	88	605	95	below_threshold
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	76.0887	89	605	95	below_threshold
Streptomyces taklimakanensis	strain=TRM43335	GCA_009709575.1	2569853	2569853	type	True	76.0878	80	605	95	below_threshold
Streptomyces albulus	strain=JCM 4718	GCA_014650635.1	68570	68570	suspected-type	True	76.0736	97	605	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	76.0706	77	605	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	76.0604	81	605	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	75.9568	100	605	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	75.9358	81	605	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	75.8833	92	605	95	below_threshold
Actinoallomurus spadix	strain=KCTC 9252	GCA_024055725.1	79912	79912	type	True	75.8811	94	605	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	75.8262	55	605	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.8006	95	605	95	below_threshold
Streptomyces thermovulgaris	strain=NRRL B-12375	GCA_002155915.1	1934	1934	type	True	75.7826	84	605	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	75.7579	60	605	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:41:55,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3199/tc_result.tsv
[2023-03-16 08:41:55,639] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:41:55,639] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:41:55,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/checkm_data
[2023-03-16 08:41:55,639] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:41:55,645] [INFO] Task started: CheckM
[2023-03-16 08:41:55,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3199/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3199/checkm_input OceanDNA-b3199/checkm_result
[2023-03-16 08:42:28,578] [INFO] Task succeeded: CheckM
[2023-03-16 08:42:28,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:42:28,617] [INFO] ===== Completeness check finished =====
[2023-03-16 08:42:28,617] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:42:28,618] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3199/markers.fasta)
[2023-03-16 08:42:28,619] [INFO] Task started: Blastn
[2023-03-16 08:42:28,619] [INFO] Running command: blastn -query OceanDNA-b3199/markers.fasta -db /var/lib/cwl/stg722da65c-acf4-4a3b-a455-876cae48ade3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3199/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:42:29,910] [INFO] Task succeeded: Blastn
[2023-03-16 08:42:29,910] [INFO] Selected 18 target genomes.
[2023-03-16 08:42:29,911] [INFO] Target genome list was writen to OceanDNA-b3199/target_genomes_gtdb.txt
[2023-03-16 08:42:30,053] [INFO] Task started: fastANI
[2023-03-16 08:42:30,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2691788-d987-4e5f-8789-6d18eb8cd9aa/OceanDNA-b3199.fa --refList OceanDNA-b3199/target_genomes_gtdb.txt --output OceanDNA-b3199/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:42:42,786] [INFO] Task succeeded: fastANI
[2023-03-16 08:42:42,795] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:42:42,796] [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
GCA_903934925.1	s__UBA10649 sp903934925	79.3473	299	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_017856385.1	s__UBA10649 sp017856385	79.2194	317	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	78.6069	284	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717115.1	s__UBA10649 sp016717115	78.2804	228	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903940375.1	s__UBA10649 sp903940375	78.0584	195	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	-
GCA_903908025.1	s__UBA10649 sp903908025	77.9562	203	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.87	97.91	0.84	0.77	3	-
GCA_017849335.1	s__UBA10649 sp017849335	77.8467	180	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009726075.1	s__WLND01 sp009726075	76.9699	106	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297305.1	s__FW305-bin1 sp004297305	76.7685	90	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__FW305-bin1;g__FW305-bin1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721155.3	s__Marihabitans melonis	76.1196	81	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	99.04	97.16	0.97	0.90	16	-
GCF_000381885.1	s__Spirillospora atramentaria	76.1011	88	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spirillospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709575.1	s__Streptomyces taklimakanensis	76.0303	83	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636295.1	s__Isoptericola dokdonensis	76.0294	61	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	76.0293	110	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	75.8833	92	605	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:42:42,804] [INFO] GTDB search result was written to OceanDNA-b3199/result_gtdb.tsv
[2023-03-16 08:42:42,817] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:42:42,820] [INFO] DFAST_QC result json was written to OceanDNA-b3199/dqc_result.json
[2023-03-16 08:42:42,820] [INFO] DFAST_QC completed!
[2023-03-16 08:42:42,820] [INFO] Total running time: 0h1m33s