[2024-01-24 12:09:05,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:09:05,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:09:05,707] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference
[2024-01-24 12:09:06,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:09:06,903] [INFO] Task started: Prodigal
[2024-01-24 12:09:06,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b76e7cd-4f37-487c-b13c-061e66578ef8/GCF_015645445.1_ASM1564544v1_genomic.fna.gz | prodigal -d GCF_015645445.1_ASM1564544v1_genomic.fna/cds.fna -a GCF_015645445.1_ASM1564544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:09:37,462] [INFO] Task succeeded: Prodigal
[2024-01-24 12:09:37,462] [INFO] Task started: HMMsearch
[2024-01-24 12:09:37,463] [INFO] Running command: hmmsearch --tblout GCF_015645445.1_ASM1564544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/reference_markers.hmm GCF_015645445.1_ASM1564544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:09:37,884] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:09:37,886] [INFO] Found 6/6 markers.
[2024-01-24 12:09:37,973] [INFO] Query marker FASTA was written to GCF_015645445.1_ASM1564544v1_genomic.fna/markers.fasta
[2024-01-24 12:09:37,973] [INFO] Task started: Blastn
[2024-01-24 12:09:37,973] [INFO] Running command: blastn -query GCF_015645445.1_ASM1564544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/reference_markers.fasta -out GCF_015645445.1_ASM1564544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:39,206] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:39,210] [INFO] Selected 18 target genomes.
[2024-01-24 12:09:39,211] [INFO] Target genome list was writen to GCF_015645445.1_ASM1564544v1_genomic.fna/target_genomes.txt
[2024-01-24 12:09:39,218] [INFO] Task started: fastANI
[2024-01-24 12:09:39,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b76e7cd-4f37-487c-b13c-061e66578ef8/GCF_015645445.1_ASM1564544v1_genomic.fna.gz --refList GCF_015645445.1_ASM1564544v1_genomic.fna/target_genomes.txt --output GCF_015645445.1_ASM1564544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:10:25,614] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:25,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:10:25,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:10:25,636] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:10:25,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:10:25,636] [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
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	100.0	3541	3566	95	conclusive
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	86.4804	2126	3566	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	85.9554	2159	3566	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	85.9421	2209	3566	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	85.8922	2067	3566	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.8904	2209	3566	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	85.8343	2060	3566	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.686	2033	3566	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.6635	2101	3566	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.6299	2290	3566	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.5487	2149	3566	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	85.41	1900	3566	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	85.3752	1989	3566	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	84.3644	1860	3566	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.0467	1939	3566	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.8029	1159	3566	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.2213	1891	3566	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	78.9729	1212	3566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:10:25,638] [INFO] DFAST Taxonomy check result was written to GCF_015645445.1_ASM1564544v1_genomic.fna/tc_result.tsv
[2024-01-24 12:10:25,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:10:25,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:10:25,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/checkm_data
[2024-01-24 12:10:25,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:10:25,738] [INFO] Task started: CheckM
[2024-01-24 12:10:25,738] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015645445.1_ASM1564544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015645445.1_ASM1564544v1_genomic.fna/checkm_input GCF_015645445.1_ASM1564544v1_genomic.fna/checkm_result
[2024-01-24 12:12:01,212] [INFO] Task succeeded: CheckM
[2024-01-24 12:12:01,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.45%
Strain heterogeneity: 81.82%
--------------------------------------------------------------------------------
[2024-01-24 12:12:01,245] [INFO] ===== Completeness check finished =====
[2024-01-24 12:12:01,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:12:01,246] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015645445.1_ASM1564544v1_genomic.fna/markers.fasta)
[2024-01-24 12:12:01,246] [INFO] Task started: Blastn
[2024-01-24 12:12:01,246] [INFO] Running command: blastn -query GCF_015645445.1_ASM1564544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeb841fd-056e-49cc-8f58-b4d8f50348ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_015645445.1_ASM1564544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:12:03,157] [INFO] Task succeeded: Blastn
[2024-01-24 12:12:03,161] [INFO] Selected 16 target genomes.
[2024-01-24 12:12:03,161] [INFO] Target genome list was writen to GCF_015645445.1_ASM1564544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:12:03,303] [INFO] Task started: fastANI
[2024-01-24 12:12:03,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b76e7cd-4f37-487c-b13c-061e66578ef8/GCF_015645445.1_ASM1564544v1_genomic.fna.gz --refList GCF_015645445.1_ASM1564544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015645445.1_ASM1564544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:12:45,714] [INFO] Task succeeded: fastANI
[2024-01-24 12:12:45,734] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:12:45,735] [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_015645445.1	s__Nonomuraea cypriaca	100.0	3541	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005893125.1	s__Nonomuraea sp005893125	86.4993	2123	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889725.1	s__Nonomuraea zeae	86.0008	2150	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	85.9124	2213	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348685.1	s__Nonomuraea deserti	85.8565	2074	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_014873145.1	s__Nonomuraea angiospora	85.8371	2220	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	85.7442	2107	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	85.6658	2034	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	85.6521	2285	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348345.1	s__Nonomuraea longispora	85.4087	1899	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_008086045.1	s__Nonomuraea sp008086045	85.054	2212	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.0057	1944	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_008017515.1	s__Nonomuraea sp008017515	82.755	1765	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862995.1	s__Acrocarpospora phusangensis	79.1514	1197	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018476525.1	s__Acrocarpospora sp018476525	78.9792	1212	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009687885.1	s__Acrocarpospora pleiomorpha	78.9727	1183	3566	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:12:45,736] [INFO] GTDB search result was written to GCF_015645445.1_ASM1564544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:12:45,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:12:45,740] [INFO] DFAST_QC result json was written to GCF_015645445.1_ASM1564544v1_genomic.fna/dqc_result.json
[2024-01-24 12:12:45,740] [INFO] DFAST_QC completed!
[2024-01-24 12:12:45,741] [INFO] Total running time: 0h3m40s