[2024-01-25 18:00:20,362] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,364] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,364] [INFO] DQC Reference Directory: /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference
[2024-01-25 18:00:21,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,514] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,514] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb62d176-b128-42c9-8ad3-44e448b1e403/GCF_024436035.1_ASM2443603v1_genomic.fna.gz | prodigal -d GCF_024436035.1_ASM2443603v1_genomic.fna/cds.fna -a GCF_024436035.1_ASM2443603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:39,762] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:39,762] [INFO] Task started: HMMsearch
[2024-01-25 18:00:39,762] [INFO] Running command: hmmsearch --tblout GCF_024436035.1_ASM2443603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/reference_markers.hmm GCF_024436035.1_ASM2443603v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:40,045] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:40,046] [INFO] Found 6/6 markers.
[2024-01-25 18:00:40,096] [INFO] Query marker FASTA was written to GCF_024436035.1_ASM2443603v1_genomic.fna/markers.fasta
[2024-01-25 18:00:40,096] [INFO] Task started: Blastn
[2024-01-25 18:00:40,096] [INFO] Running command: blastn -query GCF_024436035.1_ASM2443603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/reference_markers.fasta -out GCF_024436035.1_ASM2443603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:41,339] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:41,341] [INFO] Selected 24 target genomes.
[2024-01-25 18:00:41,342] [INFO] Target genome list was writen to GCF_024436035.1_ASM2443603v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:41,357] [INFO] Task started: fastANI
[2024-01-25 18:00:41,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb62d176-b128-42c9-8ad3-44e448b1e403/GCF_024436035.1_ASM2443603v1_genomic.fna.gz --refList GCF_024436035.1_ASM2443603v1_genomic.fna/target_genomes.txt --output GCF_024436035.1_ASM2443603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:22,612] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:22,613] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:22,614] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:22,628] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:01:22,628] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:01:22,628] [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
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	82.3152	1153	2320	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	82.2477	1201	2320	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	81.1308	769	2320	95	below_threshold
Streptomyces olivoverticillatus	strain=CECT 3266	GCA_014203555.1	66427	66427	type	True	80.9117	919	2320	95	below_threshold
Streptomyces roseifaciens	strain=MBT76	GCA_001445655.1	1488406	1488406	type	True	80.5163	1004	2320	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	80.5086	963	2320	95	below_threshold
Streptomyces mashuensis	strain=JCM 4059	GCA_014654785.1	33904	33904	type	True	80.4738	927	2320	95	below_threshold
Streptomyces abikoensis	strain=JCM 4002	GCA_014648775.1	97398	97398	type	True	80.4308	974	2320	95	below_threshold
Streptomyces hiroshimensis	strain=JCM 4586	GCA_014650335.1	66424	66424	type	True	80.4032	966	2320	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	80.3826	979	2320	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	80.3667	1043	2320	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	80.3492	983	2320	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	80.2768	954	2320	95	below_threshold
Streptomyces monomycini	strain=NRRL B-24309	GCA_000715845.1	371720	371720	type	True	80.2107	995	2320	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	80.1963	1028	2320	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	80.1916	957	2320	95	below_threshold
Streptomyces kasugaensis	strain=BCRC 12349	GCA_002261115.1	1946	1946	type	True	80.1651	1014	2320	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.1572	983	2320	95	below_threshold
Streptomyces inhibens	strain=NEAU-D10	GCA_003389455.1	2293571	2293571	type	True	80.1569	1021	2320	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	80.1426	1001	2320	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	80.0744	1027	2320	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.0619	1081	2320	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	80.0482	882	2320	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	79.9681	998	2320	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:22,629] [INFO] DFAST Taxonomy check result was written to GCF_024436035.1_ASM2443603v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:22,630] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:22,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:22,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/checkm_data
[2024-01-25 18:01:22,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:22,698] [INFO] Task started: CheckM
[2024-01-25 18:01:22,698] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024436035.1_ASM2443603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024436035.1_ASM2443603v1_genomic.fna/checkm_input GCF_024436035.1_ASM2443603v1_genomic.fna/checkm_result
[2024-01-25 18:02:35,466] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:35,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:35,502] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:35,502] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:35,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024436035.1_ASM2443603v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:35,503] [INFO] Task started: Blastn
[2024-01-25 18:02:35,503] [INFO] Running command: blastn -query GCF_024436035.1_ASM2443603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ef04ab-0c94-4ae9-9aba-96e630a92737/dqc_reference/reference_markers_gtdb.fasta -out GCF_024436035.1_ASM2443603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:37,671] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:37,674] [INFO] Selected 23 target genomes.
[2024-01-25 18:02:37,674] [INFO] Target genome list was writen to GCF_024436035.1_ASM2443603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:37,696] [INFO] Task started: fastANI
[2024-01-25 18:02:37,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb62d176-b128-42c9-8ad3-44e448b1e403/GCF_024436035.1_ASM2443603v1_genomic.fna.gz --refList GCF_024436035.1_ASM2443603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024436035.1_ASM2443603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:14,452] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:14,466] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:03:14,466] [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_019243445.1	s__Streptomyces sp019243445	85.8749	879	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003144095.1	s__Streptomyces sp003144095	82.4879	1144	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000240165.1	s__Streptomyces cattleya	81.9299	1185	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001418495.1	s__Streptomyces pathocidini	81.155	767	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719265.1	s__Streptomyces roseoverticillatus	80.5306	957	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2548	N/A	N/A	N/A	N/A	1	-
GCF_003626645.1	s__Streptomyces klenkii	80.5213	961	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.37	99.37	0.96	0.96	2	-
GCF_000719865.1	s__Streptomyces albus_E	80.5042	861	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654785.1	s__Streptomyces mashuensis	80.4777	926	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007595705.1	s__Streptomyces sp007595705	80.4729	1002	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717345.1	s__Streptomyces lydicus	80.4519	1054	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.38	0.95	0.89	6	-
GCF_900142575.1	s__Streptomyces paucisporeus	80.3938	978	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103985.1	s__Streptomyces guanduensis	80.3871	975	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070345.1	s__Streptomyces sp018070345	80.386	863	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701325.1	s__Streptomyces sp000701325	80.2955	955	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553455.1	s__Streptomyces hygroscopicus	80.2652	954	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCA_000721275.1	s__Streptomyces sp000721275	80.2218	935	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	80.21	954	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_001905005.1	s__Streptomyces sp001905005	80.2054	1019	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110255.1	s__Streptomyces rubidus	80.1951	1026	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003389455.1	s__Streptomyces inhibens	80.1883	1015	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000720995.1	s__Streptomyces celluloflavus	80.1834	990	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.24	98.62	0.95	0.89	4	-
GCF_014646055.1	s__Streptomyces_A tyrosinilyticus	80.1277	958	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	80.0792	1026	2320	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:14,470] [INFO] GTDB search result was written to GCF_024436035.1_ASM2443603v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:14,470] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:14,474] [INFO] DFAST_QC result json was written to GCF_024436035.1_ASM2443603v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:14,475] [INFO] DFAST_QC completed!
[2024-01-25 18:03:14,475] [INFO] Total running time: 0h2m54s