[2024-01-24 13:37:25,943] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:25,944] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:25,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference
[2024-01-24 13:37:27,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:27,168] [INFO] Task started: Prodigal
[2024-01-24 13:37:27,168] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa580051-b014-4e34-8da2-e4f95504d027/GCF_013280595.1_4NS15_2019_02_14_genomic.fna.gz | prodigal -d GCF_013280595.1_4NS15_2019_02_14_genomic.fna/cds.fna -a GCF_013280595.1_4NS15_2019_02_14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:38:18,194] [INFO] Task succeeded: Prodigal
[2024-01-24 13:38:18,194] [INFO] Task started: HMMsearch
[2024-01-24 13:38:18,195] [INFO] Running command: hmmsearch --tblout GCF_013280595.1_4NS15_2019_02_14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/reference_markers.hmm GCF_013280595.1_4NS15_2019_02_14_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:38:18,566] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:38:18,567] [INFO] Found 6/6 markers.
[2024-01-24 13:38:18,641] [INFO] Query marker FASTA was written to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/markers.fasta
[2024-01-24 13:38:18,641] [INFO] Task started: Blastn
[2024-01-24 13:38:18,641] [INFO] Running command: blastn -query GCF_013280595.1_4NS15_2019_02_14_genomic.fna/markers.fasta -db /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/reference_markers.fasta -out GCF_013280595.1_4NS15_2019_02_14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:19,869] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:19,872] [INFO] Selected 16 target genomes.
[2024-01-24 13:38:19,872] [INFO] Target genome list was writen to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/target_genomes.txt
[2024-01-24 13:38:19,913] [INFO] Task started: fastANI
[2024-01-24 13:38:19,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa580051-b014-4e34-8da2-e4f95504d027/GCF_013280595.1_4NS15_2019_02_14_genomic.fna.gz --refList GCF_013280595.1_4NS15_2019_02_14_genomic.fna/target_genomes.txt --output GCF_013280595.1_4NS15_2019_02_14_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:53,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:53,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:53,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:53,643] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:53,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:53,643] [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
Kibdelosporangium persicum	strain=4NS15	GCA_013280595.1	2698649	2698649	type	True	100.0	3392	3404	95	conclusive
Kibdelosporangium aridum	strain=DSM 43828	GCA_900176515.1	2030	2030	type	True	85.7528	2302	3404	95	below_threshold
Kibdelosporangium phytohabitans	strain=KLBMP1111	GCA_001302585.1	860235	860235	type	True	84.7949	2077	3404	95	below_threshold
Kibdelosporangium philippinense	strain=ATCC 49844	GCA_021390435.3	211113	211113	type	True	84.6088	1976	3404	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	82.6809	1872	3404	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.7227	930	3404	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	78.6963	1115	3404	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.6494	894	3404	95	below_threshold
Actinokineospora iranica	strain=IBRC-M 10403	GCA_900101685.1	1271860	1271860	type	True	78.5924	853	3404	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	78.588	860	3404	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	78.49	962	3404	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	78.3979	1108	3404	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	78.3141	1158	3404	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	78.1916	915	3404	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.1837	1142	3404	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	77.893	844	3404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:53,644] [INFO] DFAST Taxonomy check result was written to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/tc_result.tsv
[2024-01-24 13:38:53,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:53,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:53,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/checkm_data
[2024-01-24 13:38:53,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:53,734] [INFO] Task started: CheckM
[2024-01-24 13:38:53,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013280595.1_4NS15_2019_02_14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013280595.1_4NS15_2019_02_14_genomic.fna/checkm_input GCF_013280595.1_4NS15_2019_02_14_genomic.fna/checkm_result
[2024-01-24 13:42:29,845] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:29,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:29,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:29,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013280595.1_4NS15_2019_02_14_genomic.fna/markers.fasta)
[2024-01-24 13:42:29,867] [INFO] Task started: Blastn
[2024-01-24 13:42:29,867] [INFO] Running command: blastn -query GCF_013280595.1_4NS15_2019_02_14_genomic.fna/markers.fasta -db /var/lib/cwl/stg52cd3e9f-40b1-47e0-9345-c8eb1cb89fd4/dqc_reference/reference_markers_gtdb.fasta -out GCF_013280595.1_4NS15_2019_02_14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:31,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:31,742] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:31,742] [INFO] Target genome list was writen to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:31,749] [INFO] Task started: fastANI
[2024-01-24 13:42:31,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa580051-b014-4e34-8da2-e4f95504d027/GCF_013280595.1_4NS15_2019_02_14_genomic.fna.gz --refList GCF_013280595.1_4NS15_2019_02_14_genomic.fna/target_genomes_gtdb.txt --output GCF_013280595.1_4NS15_2019_02_14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:03,643] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:03,652] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:03,652] [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_013280595.1	s__Kibdelosporangium persicum	100.0	3391	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000720375.1	s__Kibdelosporangium sp000720375	85.7937	2263	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900176515.1	s__Kibdelosporangium aridum	85.757	2303	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001302585.1	s__Kibdelosporangium phytohabitans	84.7976	2075	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000826545.1	s__Kibdelosporangium sp000826545	84.7373	2015	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984155.1	s__Kibdelosporangium sp001984155	84.648	2057	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876405.1	s__Kibdelosporangium banguiense	82.6642	1876	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Kibdelosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345645.1	s__Actinocrispum wychmicini	81.0074	1546	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinocrispum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	78.6575	1131	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_900101685.1	s__Actinokineospora iranica	78.5953	852	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362825.1	s__Labedaea rhizosphaerae	78.5796	983	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Labedaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	78.2248	902	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	78.1681	921	3404	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:03,653] [INFO] GTDB search result was written to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:03,654] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:03,657] [INFO] DFAST_QC result json was written to GCF_013280595.1_4NS15_2019_02_14_genomic.fna/dqc_result.json
[2024-01-24 13:43:03,657] [INFO] DFAST_QC completed!
[2024-01-24 13:43:03,657] [INFO] Total running time: 0h5m38s