[2024-01-24 13:09:41,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:41,285] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:41,286] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference
[2024-01-24 13:09:42,567] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:42,568] [INFO] Task started: Prodigal
[2024-01-24 13:09:42,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg495e092e-5aa8-446d-a1ab-53154fab48af/GCF_000024865.1_ASM2486v1_genomic.fna.gz | prodigal -d GCF_000024865.1_ASM2486v1_genomic.fna/cds.fna -a GCF_000024865.1_ASM2486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:13,383] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:13,384] [INFO] Task started: HMMsearch
[2024-01-24 13:10:13,384] [INFO] Running command: hmmsearch --tblout GCF_000024865.1_ASM2486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/reference_markers.hmm GCF_000024865.1_ASM2486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:13,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:13,753] [INFO] Found 6/6 markers.
[2024-01-24 13:10:13,843] [INFO] Query marker FASTA was written to GCF_000024865.1_ASM2486v1_genomic.fna/markers.fasta
[2024-01-24 13:10:13,844] [INFO] Task started: Blastn
[2024-01-24 13:10:13,844] [INFO] Running command: blastn -query GCF_000024865.1_ASM2486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/reference_markers.fasta -out GCF_000024865.1_ASM2486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:15,267] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:15,271] [INFO] Selected 15 target genomes.
[2024-01-24 13:10:15,272] [INFO] Target genome list was writen to GCF_000024865.1_ASM2486v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:15,278] [INFO] Task started: fastANI
[2024-01-24 13:10:15,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg495e092e-5aa8-446d-a1ab-53154fab48af/GCF_000024865.1_ASM2486v1_genomic.fna.gz --refList GCF_000024865.1_ASM2486v1_genomic.fna/target_genomes.txt --output GCF_000024865.1_ASM2486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:51,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:51,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:51,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:51,269] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:51,269] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:51,269] [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
Streptosporangium roseum	strain=DSM 43021	GCA_000024865.1	2001	2001	type	True	100.0	3454	3456	95	conclusive
Streptosporangium canum	strain=CGMCC 4.2126	GCA_900113865.1	324952	324952	type	True	94.7267	2628	3456	95	below_threshold
Streptosporangium minutum	strain=M26	GCA_002149035.1	569862	569862	type	True	94.6237	2508	3456	95	below_threshold
Streptosporangium album	strain=DSM 43023	GCA_014203795.1	47479	47479	type	True	88.4544	1984	3456	95	below_threshold
Streptosporangium amethystogenes	strain=NRRL B-2639	GCA_000721075.1	2002	2002	type	True	85.192	1919	3456	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	84.9028	1811	3456	95	below_threshold
Planomonospora parontospora subsp. antibiotica	strain=NBRC 15869	GCA_016863235.1	97193	58119	type	True	84.5184	1688	3456	95	below_threshold
Planomonospora sphaerica	strain=JCM 9374	GCA_001653075.1	161355	161355	type	True	84.4368	1750	3456	95	below_threshold
Planobispora longispora	strain=NBRC 13918	GCA_016863135.1	28887	28887	type	True	84.1727	1843	3456	95	below_threshold
Planobispora rosea	strain=NBRC 15558	GCA_016863155.1	35762	35762	type	True	84.1704	1763	3456	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	80.515	1659	3456	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	80.3899	1065	3456	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	80.0885	1569	3456	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	80.0777	1629	3456	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	80.0292	1579	3456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:51,271] [INFO] DFAST Taxonomy check result was written to GCF_000024865.1_ASM2486v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:51,271] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:51,271] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:51,272] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/checkm_data
[2024-01-24 13:10:51,273] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:51,360] [INFO] Task started: CheckM
[2024-01-24 13:10:51,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024865.1_ASM2486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024865.1_ASM2486v1_genomic.fna/checkm_input GCF_000024865.1_ASM2486v1_genomic.fna/checkm_result
[2024-01-24 13:12:44,076] [INFO] Task succeeded: CheckM
[2024-01-24 13:12:44,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:12:44,097] [INFO] ===== Completeness check finished =====
[2024-01-24 13:12:44,097] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:12:44,097] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024865.1_ASM2486v1_genomic.fna/markers.fasta)
[2024-01-24 13:12:44,098] [INFO] Task started: Blastn
[2024-01-24 13:12:44,098] [INFO] Running command: blastn -query GCF_000024865.1_ASM2486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9937ca2-abcd-4f74-ae1e-a0a9e77b98ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024865.1_ASM2486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:46,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:46,168] [INFO] Selected 10 target genomes.
[2024-01-24 13:12:46,168] [INFO] Target genome list was writen to GCF_000024865.1_ASM2486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:12:46,260] [INFO] Task started: fastANI
[2024-01-24 13:12:46,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg495e092e-5aa8-446d-a1ab-53154fab48af/GCF_000024865.1_ASM2486v1_genomic.fna.gz --refList GCF_000024865.1_ASM2486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024865.1_ASM2486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:11,010] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:11,019] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:11,019] [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_000024865.1	s__Streptosporangium roseum	100.0	3452	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900113865.1	s__Streptosporangium canum	94.7166	2630	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	96.48	96.48	0.86	0.86	2	-
GCF_002149035.1	s__Streptosporangium minutum	94.6525	2504	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.8736	N/A	N/A	N/A	N/A	1	-
GCF_014203795.1	s__Streptosporangium album	88.4388	1986	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188345.1	s__Streptosporangium subroseum	86.0231	2011	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	95.81	95.81	0.87	0.87	2	-
GCF_000721075.1	s__Streptosporangium amethystogenes	85.1836	1921	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015711605.1	s__Planomonospora_A sp015711605	84.9024	1776	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	84.8424	1798	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648175.1	s__Planobispora rosea	84.2002	1775	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planobispora	95.0	99.82	99.64	0.97	0.95	3	-
GCF_015690345.1	s__Plantactinospora sp015690345	76.3562	729	3456	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:11,021] [INFO] GTDB search result was written to GCF_000024865.1_ASM2486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:11,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:11,025] [INFO] DFAST_QC result json was written to GCF_000024865.1_ASM2486v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:11,025] [INFO] DFAST_QC completed!
[2024-01-24 13:13:11,025] [INFO] Total running time: 0h3m30s