[2024-01-24 14:05:36,772] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,774] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference
[2024-01-24 14:05:38,119] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,121] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,122] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9d71804-c615-44c3-878e-ea97a7f79b77/GCF_014203695.1_ASM1420369v1_genomic.fna.gz | prodigal -d GCF_014203695.1_ASM1420369v1_genomic.fna/cds.fna -a GCF_014203695.1_ASM1420369v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:52,978] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:52,979] [INFO] Task started: HMMsearch
[2024-01-24 14:05:52,979] [INFO] Running command: hmmsearch --tblout GCF_014203695.1_ASM1420369v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/reference_markers.hmm GCF_014203695.1_ASM1420369v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:53,301] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:53,302] [INFO] Found 6/6 markers.
[2024-01-24 14:05:53,343] [INFO] Query marker FASTA was written to GCF_014203695.1_ASM1420369v1_genomic.fna/markers.fasta
[2024-01-24 14:05:53,343] [INFO] Task started: Blastn
[2024-01-24 14:05:53,343] [INFO] Running command: blastn -query GCF_014203695.1_ASM1420369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/reference_markers.fasta -out GCF_014203695.1_ASM1420369v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:54,626] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:54,629] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:54,630] [INFO] Target genome list was writen to GCF_014203695.1_ASM1420369v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:54,654] [INFO] Task started: fastANI
[2024-01-24 14:05:54,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9d71804-c615-44c3-878e-ea97a7f79b77/GCF_014203695.1_ASM1420369v1_genomic.fna.gz --refList GCF_014203695.1_ASM1420369v1_genomic.fna/target_genomes.txt --output GCF_014203695.1_ASM1420369v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:18,198] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:18,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:18,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:18,212] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:18,212] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:18,212] [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
Nocardiopsis algeriensis	strain=CECT 8712	GCA_014203695.1	1478215	1478215	type	True	100.0	1591	1592	95	conclusive
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	84.3031	1125	1592	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	84.2892	1179	1592	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	84.2744	1180	1592	95	below_threshold
Nocardiopsis deserti	strain=H13	GCA_008638355.1	2605988	2605988	type	True	84.2568	1179	1592	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	84.2325	1021	1592	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	84.2116	1175	1592	95	below_threshold
Nocardiopsis quinghaiensis	strain=YIM 28A4	GCA_008638365.1	464995	464995	type	True	84.1882	1129	1592	95	below_threshold
Nocardiopsis alborubida	strain=NBRC 13392	GCA_001552695.1	146802	146802	type	True	84.1559	1180	1592	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	84.0604	1163	1592	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	84.0586	1185	1592	95	below_threshold
Nocardiopsis halotolerans	strain=DSM 44410	GCA_000341065.1	124252	124252	type	True	83.758	1075	1592	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	82.7955	1077	1592	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	81.8696	976	1592	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3276	893	1592	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.8675	724	1592	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.5347	715	1592	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:18,214] [INFO] DFAST Taxonomy check result was written to GCF_014203695.1_ASM1420369v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:18,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:18,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:18,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/checkm_data
[2024-01-24 14:06:18,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:18,263] [INFO] Task started: CheckM
[2024-01-24 14:06:18,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014203695.1_ASM1420369v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014203695.1_ASM1420369v1_genomic.fna/checkm_input GCF_014203695.1_ASM1420369v1_genomic.fna/checkm_result
[2024-01-24 14:07:26,317] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:26,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,346] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:26,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:26,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014203695.1_ASM1420369v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:26,347] [INFO] Task started: Blastn
[2024-01-24 14:07:26,347] [INFO] Running command: blastn -query GCF_014203695.1_ASM1420369v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a151e9-04e3-4c9c-8e0b-51a88bacc08d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014203695.1_ASM1420369v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:28,390] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:28,394] [INFO] Selected 15 target genomes.
[2024-01-24 14:07:28,394] [INFO] Target genome list was writen to GCF_014203695.1_ASM1420369v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:28,412] [INFO] Task started: fastANI
[2024-01-24 14:07:28,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9d71804-c615-44c3-878e-ea97a7f79b77/GCF_014203695.1_ASM1420369v1_genomic.fna.gz --refList GCF_014203695.1_ASM1420369v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014203695.1_ASM1420369v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:49,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:49,718] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:49,719] [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_014203695.1	s__Nocardiopsis algeriensis	100.0	1591	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002529455.1	s__Nocardiopsis fusca	84.4456	1166	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	84.2703	1181	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_001905145.1	s__Nocardiopsis sp001905145	84.264	1175	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396365.1	s__Nocardiopsis alborubida	84.197	1176	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.95	95.06	0.88	0.80	4	-
GCA_018316655.1	s__Nocardiopsis sp018316655	84.1812	1185	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008638365.1	s__Nocardiopsis quinghaiensis	84.166	1134	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009830945.1	s__Nocardiopsis sp009830945	84.1078	1144	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
GCF_900141985.1	s__Nocardiopsis flavescens	84.0716	1162	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	84.0016	1179	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_000341065.1	s__Nocardiopsis halotolerans	83.7455	1075	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	83.0062	1026	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634495.1	s__Nocardiopsis sp003634495	82.8777	1089	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340985.1	s__Nocardiopsis valliformis	82.6727	1050	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014892575.1	s__Nocardiopsis coralli	81.862	977	1592	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:49,720] [INFO] GTDB search result was written to GCF_014203695.1_ASM1420369v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:49,721] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:49,734] [INFO] DFAST_QC result json was written to GCF_014203695.1_ASM1420369v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:49,734] [INFO] DFAST_QC completed!
[2024-01-24 14:07:49,734] [INFO] Total running time: 0h2m13s