[2023-06-29 11:31:52,305] [INFO] DFAST_QC pipeline started.
[2023-06-29 11:31:52,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 11:31:52,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference
[2023-06-29 11:31:53,700] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 11:31:53,701] [INFO] Task started: Prodigal
[2023-06-29 11:31:53,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f8e9d42-dbbd-47c9-b4dc-90c450f108dd/GCA_005885085.1_ASM588508v1_genomic.fna.gz | prodigal -d GCA_005885085.1_ASM588508v1_genomic.fna/cds.fna -a GCA_005885085.1_ASM588508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 11:32:06,448] [INFO] Task succeeded: Prodigal
[2023-06-29 11:32:06,449] [INFO] Task started: HMMsearch
[2023-06-29 11:32:06,449] [INFO] Running command: hmmsearch --tblout GCA_005885085.1_ASM588508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/reference_markers.hmm GCA_005885085.1_ASM588508v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 11:32:06,702] [INFO] Task succeeded: HMMsearch
[2023-06-29 11:32:06,704] [INFO] Found 6/6 markers.
[2023-06-29 11:32:06,737] [INFO] Query marker FASTA was written to GCA_005885085.1_ASM588508v1_genomic.fna/markers.fasta
[2023-06-29 11:32:06,738] [INFO] Task started: Blastn
[2023-06-29 11:32:06,738] [INFO] Running command: blastn -query GCA_005885085.1_ASM588508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/reference_markers.fasta -out GCA_005885085.1_ASM588508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:32:07,500] [INFO] Task succeeded: Blastn
[2023-06-29 11:32:07,506] [INFO] Selected 22 target genomes.
[2023-06-29 11:32:07,507] [INFO] Target genome list was writen to GCA_005885085.1_ASM588508v1_genomic.fna/target_genomes.txt
[2023-06-29 11:32:07,513] [INFO] Task started: fastANI
[2023-06-29 11:32:07,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f8e9d42-dbbd-47c9-b4dc-90c450f108dd/GCA_005885085.1_ASM588508v1_genomic.fna.gz --refList GCA_005885085.1_ASM588508v1_genomic.fna/target_genomes.txt --output GCA_005885085.1_ASM588508v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 11:32:23,617] [INFO] Task succeeded: fastANI
[2023-06-29 11:32:23,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 11:32:23,618] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 11:32:23,630] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 11:32:23,631] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 11:32:23,631] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	77.3786	242	730	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.5227	213	730	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.4858	192	730	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.4317	114	730	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	75.4228	135	730	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.3849	135	730	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.3801	173	730	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.2886	144	730	95	below_threshold
Patulibacter medicamentivorans	strain=I11	GCA_000240225.2	1097667	1097667	type	True	75.0918	127	730	95	below_threshold
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	75.0833	96	730	95	below_threshold
Microbispora corallina	strain=NBRC 16416	GCA_016863035.1	83302	83302	type	True	75.0107	120	730	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	74.9789	126	730	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	74.8942	58	730	95	below_threshold
Gryllotalpicola protaetiae	strain=2DFW10M-5	GCA_003627055.1	2419771	2419771	type	True	74.8334	70	730	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 11:32:23,633] [INFO] DFAST Taxonomy check result was written to GCA_005885085.1_ASM588508v1_genomic.fna/tc_result.tsv
[2023-06-29 11:32:23,634] [INFO] ===== Taxonomy check completed =====
[2023-06-29 11:32:23,634] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 11:32:23,634] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/checkm_data
[2023-06-29 11:32:23,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 11:32:23,668] [INFO] Task started: CheckM
[2023-06-29 11:32:23,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005885085.1_ASM588508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005885085.1_ASM588508v1_genomic.fna/checkm_input GCA_005885085.1_ASM588508v1_genomic.fna/checkm_result
[2023-06-29 11:32:53,269] [INFO] Task succeeded: CheckM
[2023-06-29 11:32:53,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 11:32:53,292] [INFO] ===== Completeness check finished =====
[2023-06-29 11:32:53,292] [INFO] ===== Start GTDB Search =====
[2023-06-29 11:32:53,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005885085.1_ASM588508v1_genomic.fna/markers.fasta)
[2023-06-29 11:32:53,293] [INFO] Task started: Blastn
[2023-06-29 11:32:53,293] [INFO] Running command: blastn -query GCA_005885085.1_ASM588508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3cb271a1-44b3-4ec6-a32b-2784091bde02/dqc_reference/reference_markers_gtdb.fasta -out GCA_005885085.1_ASM588508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 11:32:54,445] [INFO] Task succeeded: Blastn
[2023-06-29 11:32:54,449] [INFO] Selected 10 target genomes.
[2023-06-29 11:32:54,450] [INFO] Target genome list was writen to GCA_005885085.1_ASM588508v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 11:32:54,462] [INFO] Task started: fastANI
[2023-06-29 11:32:54,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f8e9d42-dbbd-47c9-b4dc-90c450f108dd/GCA_005885085.1_ASM588508v1_genomic.fna.gz --refList GCA_005885085.1_ASM588508v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005885085.1_ASM588508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 11:32:59,695] [INFO] Task succeeded: fastANI
[2023-06-29 11:32:59,711] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 11:32:59,711] [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_005885085.1	s__3-1-20CM-4-69-9 sp005885085	100.0	719	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001920085.1	s__3-1-20CM-4-69-9 sp001920085	81.8002	345	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888435.1	s__3-1-20CM-4-69-9 sp005888435	81.6118	430	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885245.1	s__3-1-20CM-4-69-9 sp005885245	80.085	460	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883355.1	s__3-1-20CM-4-69-9 sp005883355	80.0213	433	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	99.31	99.31	0.92	0.92	2	-
GCA_013816245.1	s__3-1-20CM-4-69-9 sp013816245	79.8837	391	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__3-1-20CM-4-69-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005885125.1	s__AC-21 sp005885125	79.5068	330	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883995.1	s__AC-21 sp005883995	79.0155	359	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-21	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883965.1	s__AC-32 sp005883965	78.0501	244	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__AC-32	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812235.1	s__JACCTU01 sp013812235	77.8527	158	730	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCTU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 11:32:59,713] [INFO] GTDB search result was written to GCA_005885085.1_ASM588508v1_genomic.fna/result_gtdb.tsv
[2023-06-29 11:32:59,714] [INFO] ===== GTDB Search completed =====
[2023-06-29 11:32:59,717] [INFO] DFAST_QC result json was written to GCA_005885085.1_ASM588508v1_genomic.fna/dqc_result.json
[2023-06-29 11:32:59,718] [INFO] DFAST_QC completed!
[2023-06-29 11:32:59,718] [INFO] Total running time: 0h1m7s