[2024-01-24 14:47:18,897] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:18,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:18,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference
[2024-01-24 14:47:20,128] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,129] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,129] [INFO] Running command: gunzip -c /var/lib/cwl/stg254c1dae-7da5-4b76-9b1e-7f2e35e1ac5c/GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/cds.fna -a GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:44,283] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:44,283] [INFO] Task started: HMMsearch
[2024-01-24 14:47:44,283] [INFO] Running command: hmmsearch --tblout GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/reference_markers.hmm GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:44,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:44,675] [INFO] Found 6/6 markers.
[2024-01-24 14:47:44,746] [INFO] Query marker FASTA was written to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:44,747] [INFO] Task started: Blastn
[2024-01-24 14:47:44,747] [INFO] Running command: blastn -query GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/reference_markers.fasta -out GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:46,064] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:46,067] [INFO] Selected 21 target genomes.
[2024-01-24 14:47:46,068] [INFO] Target genome list was writen to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:46,076] [INFO] Task started: fastANI
[2024-01-24 14:47:46,076] [INFO] Running command: fastANI --query /var/lib/cwl/stg254c1dae-7da5-4b76-9b1e-7f2e35e1ac5c/GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna.gz --refList GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:31,887] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:31,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:31,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:31,908] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:31,909] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:31,909] [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 alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	100.0	2732	2734	95	conclusive
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	84.4371	1349	2734	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	84.2143	1610	2734	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	84.1941	1573	2734	95	below_threshold
Actinacidiphila rubida	strain=CGMCC 4.2026	GCA_900110255.1	310780	310780	type	True	83.717	1630	2734	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	83.6571	1595	2734	95	below_threshold
Actinacidiphila guanduensis	strain=CGMCC 4.2022	GCA_900103985.1	310781	310781	type	True	83.2539	1533	2734	95	below_threshold
Actinacidiphila yanglinensis	strain=CGMCC 4.2023	GCA_900107965.1	310779	310779	type	True	83.2361	1663	2734	95	below_threshold
Actinacidiphila acididurans	strain=KK5PA1	GCA_016918855.1	2784346	2784346	type	True	83.1912	1636	2734	95	below_threshold
Actinacidiphila yeochonensis	strain=CN732	GCA_000745345.1	89050	89050	type	True	82.2997	1422	2734	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	81.333	820	2734	95	below_threshold
Actinacidiphila oryziradicis	strain=NEAU-C40	GCA_005047355.1	2571141	2571141	type	True	80.3689	1300	2734	95	below_threshold
Streptomyces albofaciens	strain=ATCC 23873	GCA_008634025.1	66866	66866	type	True	80.3517	1272	2734	95	below_threshold
Streptomyces varsoviensis	strain=NRRL B-3589	GCA_000719255.1	67373	67373	type	True	80.1826	1257	2734	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	79.9984	998	2734	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	79.8414	1249	2734	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	79.6849	1211	2734	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	79.4302	1281	2734	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	79.1161	1200	2734	95	below_threshold
Kitasatospora setae	strain=NRRL B-16185	GCA_000716965.1	2066	2066	type	True	79.0428	1185	2734	95	below_threshold
Kitasatospora humi	strain=RB6PN24	GCA_020907985.1	2893891	2893891	type	True	79.0361	1012	2734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:31,924] [INFO] DFAST Taxonomy check result was written to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:48:31,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:31,926] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:31,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/checkm_data
[2024-01-24 14:48:31,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:32,007] [INFO] Task started: CheckM
[2024-01-24 14:48:32,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/checkm_input GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:50:31,141] [INFO] Task succeeded: CheckM
[2024-01-24 14:50:31,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:50:31,189] [INFO] ===== Completeness check finished =====
[2024-01-24 14:50:31,189] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:50:31,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:50:31,190] [INFO] Task started: Blastn
[2024-01-24 14:50:31,190] [INFO] Running command: blastn -query GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg426df035-2108-4c55-be30-1835fb30b8ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:50:33,321] [INFO] Task succeeded: Blastn
[2024-01-24 14:50:33,326] [INFO] Selected 18 target genomes.
[2024-01-24 14:50:33,326] [INFO] Target genome list was writen to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:50:33,346] [INFO] Task started: fastANI
[2024-01-24 14:50:33,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg254c1dae-7da5-4b76-9b1e-7f2e35e1ac5c/GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna.gz --refList GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:11,570] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:11,584] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:11,585] [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_900112845.1	s__Streptomyces alni	100.0	2731	2734	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_014596445.1	s__Streptomyces sp014596445	88.5955	1854	2734	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	84.2043	1612	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900091855.1	s__Streptomyces sp900091855	83.9499	1325	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000701325.1	s__Streptomyces sp000701325	83.8764	1482	2734	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	83.7043	1632	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783685.1	s__Streptomyces sp009783685	83.5745	1060	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000721495.1	s__Streptomyces sp000721495	83.261	1533	2734	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	83.2571	1531	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107965.1	s__Streptomyces yanglinensis	83.192	1672	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918855.1	s__Streptomyces acididurans	83.1662	1643	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756395.1	s__Streptomyces sp016756395	83.0684	1611	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745345.1	s__Streptomyces yeochonensis	82.3488	1413	2734	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	82.0997	1438	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	98.63	0.90	0.87	4	-
GCF_003999195.1	s__Streptomyces sp003999195	81.2729	1197	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000718635.1	s__Streptomyces varsoviensis	80.2015	1249	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_012726235.1	s__Streptomyces sp012726235	79.8487	1057	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717185.1	s__Kitasatospora phosalacinea_A	79.121	1187	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:11,586] [INFO] GTDB search result was written to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:11,587] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:11,596] [INFO] DFAST_QC result json was written to GCF_900112845.1_IMG-taxon_2667527403_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:51:11,597] [INFO] DFAST_QC completed!
[2024-01-24 14:51:11,597] [INFO] Total running time: 0h3m53s