[2024-01-24 14:06:14,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:14,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:14,125] [INFO] DQC Reference Directory: /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference
[2024-01-24 14:06:15,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:15,532] [INFO] Task started: Prodigal
[2024-01-24 14:06:15,532] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9c36bd1-6c9c-42f6-9300-39691b3b1e95/GCF_005047355.1_ASM504735v1_genomic.fna.gz | prodigal -d GCF_005047355.1_ASM504735v1_genomic.fna/cds.fna -a GCF_005047355.1_ASM504735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:49,904] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:49,904] [INFO] Task started: HMMsearch
[2024-01-24 14:06:49,904] [INFO] Running command: hmmsearch --tblout GCF_005047355.1_ASM504735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/reference_markers.hmm GCF_005047355.1_ASM504735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:50,374] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:50,375] [INFO] Found 6/6 markers.
[2024-01-24 14:06:50,468] [INFO] Query marker FASTA was written to GCF_005047355.1_ASM504735v1_genomic.fna/markers.fasta
[2024-01-24 14:06:50,469] [INFO] Task started: Blastn
[2024-01-24 14:06:50,469] [INFO] Running command: blastn -query GCF_005047355.1_ASM504735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/reference_markers.fasta -out GCF_005047355.1_ASM504735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:51,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:51,803] [INFO] Selected 33 target genomes.
[2024-01-24 14:06:51,804] [INFO] Target genome list was writen to GCF_005047355.1_ASM504735v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:51,833] [INFO] Task started: fastANI
[2024-01-24 14:06:51,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c36bd1-6c9c-42f6-9300-39691b3b1e95/GCF_005047355.1_ASM504735v1_genomic.fna.gz --refList GCF_005047355.1_ASM504735v1_genomic.fna/target_genomes.txt --output GCF_005047355.1_ASM504735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:51,019] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:51,020] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:51,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:51,049] [INFO] Found 33 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:51,049] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:51,049] [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
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	100.0	3635	3656	95	conclusive
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	80.3829	1041	3656	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	80.2367	1112	3656	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	80.1828	1196	3656	95	below_threshold
Streptomyces sparsogenes	strain=ATCC 25498	GCA_001704635.1	67365	67365	type	True	79.9797	1204	3656	95	below_threshold
Streptomyces sparsogenes	strain=DSM 40356	GCA_001969965.1	67365	67365	type	True	79.9787	1162	3656	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	79.8702	1214	3656	95	below_threshold
Streptomyces milbemycinicus	strain=NRRL 5739	GCA_002154605.1	476552	476552	type	True	79.7577	1159	3656	95	below_threshold
Streptomyces hygroscopicus subsp. hygroscopicus	strain=NBRC 13472	GCA_001553455.1	68042	1912	type	True	79.6742	1171	3656	95	below_threshold
Streptomyces recifensis	strain=NRRL B-3811	GCA_002154615.1	67355	67355	type	True	79.6242	847	3656	95	below_threshold
Streptomyces roseolilacinus	strain=JCM 4335	GCA_014649335.1	66904	66904	type	True	79.6	1023	3656	95	below_threshold
Streptomyces cinereoruber	strain=JCM4205	GCA_019880525.1	67260	67260	type	True	79.5882	1053	3656	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	79.5859	1107	3656	95	below_threshold
Streptomyces cinereoruber	strain=ATCC 19740	GCA_009299385.1	67260	67260	type	True	79.5821	1076	3656	95	below_threshold
Streptomyces javensis	strain=DSM 41764	GCA_016103505.1	114698	114698	type	True	79.5644	1078	3656	95	below_threshold
Streptomyces cinereoruber	strain=JCM 4205	GCA_014649095.1	67260	67260	type	True	79.5461	1063	3656	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_014656035.1	29306	29306	type	True	79.4985	1043	3656	95	below_threshold
Streptomyces griseoluteus	strain=JCM 4765	GCA_004784465.1	29306	29306	type	True	79.4855	1061	3656	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	79.4613	1213	3656	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	79.456	1096	3656	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	79.4194	1118	3656	95	below_threshold
Streptomyces populi	strain=A249	GCA_002911015.1	2058924	2058924	type	True	79.4074	1201	3656	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	79.405	1227	3656	95	below_threshold
Streptomyces triticiradicis	strain=NEAU-H2	GCA_008868685.1	2651189	2651189	type	True	79.3998	1232	3656	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	79.3931	1112	3656	95	below_threshold
Streptomyces adustus	strain=NBRC 109810	GCA_009377175.1	1609272	1609272	type	True	79.3679	1238	3656	95	below_threshold
Streptomyces zhihengii	strain=YIM T102	GCA_016919245.1	1818004	1818004	type	True	79.2066	1205	3656	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	79.1749	1270	3656	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	79.1529	1053	3656	95	below_threshold
Streptomyces albus subsp. albus	strain=NRRL B-1811	GCA_000725885.1	67257	1888	suspected-type	True	78.817	959	3656	95	below_threshold
Streptacidiphilus pinicola	strain=MMS16-CNU450	GCA_003258295.1	2219663	2219663	type	True	78.3731	972	3656	95	below_threshold
Streptacidiphilus jiangxiensis	strain=CGMCC 4.1857	GCA_900109465.1	235985	235985	type	True	78.2018	1017	3656	95	below_threshold
Streptacidiphilus jiangxiensis	strain=NBRC 100920	GCA_000787795.1	235985	235985	type	True	78.199	1032	3656	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:51,051] [INFO] DFAST Taxonomy check result was written to GCF_005047355.1_ASM504735v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:51,051] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:51,051] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:51,052] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/checkm_data
[2024-01-24 14:07:51,053] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:51,154] [INFO] Task started: CheckM
[2024-01-24 14:07:51,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005047355.1_ASM504735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005047355.1_ASM504735v1_genomic.fna/checkm_input GCF_005047355.1_ASM504735v1_genomic.fna/checkm_result
[2024-01-24 14:09:23,614] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:23,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:23,644] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:23,644] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:23,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005047355.1_ASM504735v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:23,645] [INFO] Task started: Blastn
[2024-01-24 14:09:23,645] [INFO] Running command: blastn -query GCF_005047355.1_ASM504735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35d09a89-c434-4b89-a34e-4702bb33168d/dqc_reference/reference_markers_gtdb.fasta -out GCF_005047355.1_ASM504735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:25,733] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:25,737] [INFO] Selected 31 target genomes.
[2024-01-24 14:09:25,737] [INFO] Target genome list was writen to GCF_005047355.1_ASM504735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:25,759] [INFO] Task started: fastANI
[2024-01-24 14:09:25,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9c36bd1-6c9c-42f6-9300-39691b3b1e95/GCF_005047355.1_ASM504735v1_genomic.fna.gz --refList GCF_005047355.1_ASM504735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005047355.1_ASM504735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:10:25,935] [INFO] Task succeeded: fastANI
[2024-01-24 14:10:25,962] [INFO] Found 31 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:10:25,962] [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_005047355.1	s__Streptomyces sp005047355	100.0	3634	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003999195.1	s__Streptomyces sp003999195	84.006	1786	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107395.1	s__Streptomyces fildesensis	81.0068	1382	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	98.63	0.90	0.87	4	-
GCF_900112845.1	s__Streptomyces alni	80.4786	1273	3656	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	80.4269	1092	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	80.2164	1189	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_018614525.1	s__Streptomyces sp018614525	80.2095	978	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142575.1	s__Streptomyces paucisporeus	80.1866	1215	3656	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	80.1743	1176	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001704635.1	s__Streptomyces sparsogenes	79.9827	1202	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.81	0.87	0.87	2	-
GCF_004795035.1	s__Streptomyces sp004795035	79.8505	1039	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002154605.1	s__Streptomyces milbemycinicus	79.7714	1156	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.93	99.93	0.99	0.99	2	-
GCF_013364155.1	s__Streptomyces sp013364155	79.7005	1204	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224125.1	s__Streptomyces sp002224125	79.6999	1334	3656	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	79.6751	1171	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.24	98.00	0.92	0.90	7	-
GCF_014649335.1	s__Streptomyces roseolilacinus	79.6112	1019	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509795.1	s__Streptomyces sp001509795	79.5797	1134	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_016741875.1	s__Streptomyces coffeae	79.5693	1158	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002946835.1	s__Streptomyces dengpaensis	79.5658	1112	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008042045.1	s__Streptomyces sp008042045	79.4791	1101	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004784465.1	s__Streptomyces griseoluteus	79.4764	1059	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	97.39	95.67	0.90	0.82	4	-
GCF_018138715.1	s__Streptomyces asiaticus	79.4734	1406	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	79.4403	1216	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_004784475.1	s__Streptomyces bauhiniae	79.4299	1056	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.3953	95.70	95.47	0.88	0.84	6	-
GCF_002911015.1	s__Streptomyces populi	79.3965	1204	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.17	95.17	0.82	0.82	2	-
GCF_009377175.1	s__Streptomyces adustus	79.3708	1241	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919245.1	s__Streptomyces zhihengii	79.2123	1204	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725885.1	s__Streptomyces albus	78.8239	958	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	97.77	0.97	0.92	14	-
GCF_003258295.1	s__Streptacidiphilus pinicola	78.4059	963	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943525.1	s__Kitasatospora sp002943525	78.2288	1005	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109465.1	s__Streptacidiphilus jiangxiensis	78.1933	1020	3656	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:10:25,966] [INFO] GTDB search result was written to GCF_005047355.1_ASM504735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:10:25,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:10:25,978] [INFO] DFAST_QC result json was written to GCF_005047355.1_ASM504735v1_genomic.fna/dqc_result.json
[2024-01-24 14:10:25,978] [INFO] DFAST_QC completed!
[2024-01-24 14:10:25,979] [INFO] Total running time: 0h4m12s