[2024-01-24 12:07:19,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:19,152] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:19,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference
[2024-01-24 12:07:20,378] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:20,379] [INFO] Task started: Prodigal
[2024-01-24 12:07:20,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e8ad705-5ffb-49f0-98e9-19cd8ae1f4fe/GCF_004348345.1_ASM434834v1_genomic.fna.gz | prodigal -d GCF_004348345.1_ASM434834v1_genomic.fna/cds.fna -a GCF_004348345.1_ASM434834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:44,524] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:44,525] [INFO] Task started: HMMsearch
[2024-01-24 12:07:44,525] [INFO] Running command: hmmsearch --tblout GCF_004348345.1_ASM434834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/reference_markers.hmm GCF_004348345.1_ASM434834v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:44,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:44,935] [INFO] Found 6/6 markers.
[2024-01-24 12:07:45,011] [INFO] Query marker FASTA was written to GCF_004348345.1_ASM434834v1_genomic.fna/markers.fasta
[2024-01-24 12:07:45,012] [INFO] Task started: Blastn
[2024-01-24 12:07:45,012] [INFO] Running command: blastn -query GCF_004348345.1_ASM434834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/reference_markers.fasta -out GCF_004348345.1_ASM434834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:46,258] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:46,263] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:46,263] [INFO] Target genome list was writen to GCF_004348345.1_ASM434834v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:46,269] [INFO] Task started: fastANI
[2024-01-24 12:07:46,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e8ad705-5ffb-49f0-98e9-19cd8ae1f4fe/GCF_004348345.1_ASM434834v1_genomic.fna.gz --refList GCF_004348345.1_ASM434834v1_genomic.fna/target_genomes.txt --output GCF_004348345.1_ASM434834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:08:23,328] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:23,329] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:08:23,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:08:23,354] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:08:23,354] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:08:23,354] [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 longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	100.0	2795	2827	95	inconclusive
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	95.0366	2452	2827	95	inconclusive
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	92.3604	2277	2827	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	92.0763	2289	2827	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.6264	2036	2827	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.619	1885	2827	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.5176	1976	2827	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.4991	1963	2827	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.4361	2016	2827	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.3448	1871	2827	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.2403	1697	2827	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	84.8644	1785	2827	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.3599	1117	2827	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.9517	1732	2827	95	below_threshold
Acrocarpospora phusangensis	strain=NBRC 108782	GCA_016862995.1	1070424	1070424	type	True	78.9788	1075	2827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:08:23,356] [INFO] DFAST Taxonomy check result was written to GCF_004348345.1_ASM434834v1_genomic.fna/tc_result.tsv
[2024-01-24 12:08:23,366] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:08:23,367] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:08:23,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/checkm_data
[2024-01-24 12:08:23,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:08:23,453] [INFO] Task started: CheckM
[2024-01-24 12:08:23,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348345.1_ASM434834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348345.1_ASM434834v1_genomic.fna/checkm_input GCF_004348345.1_ASM434834v1_genomic.fna/checkm_result
[2024-01-24 12:09:41,783] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:41,784] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:41,814] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:41,814] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:41,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348345.1_ASM434834v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:41,815] [INFO] Task started: Blastn
[2024-01-24 12:09:41,815] [INFO] Running command: blastn -query GCF_004348345.1_ASM434834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d8cd3ea-d798-4e1e-a5f2-8a6a4ecb90fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348345.1_ASM434834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:43,830] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:43,835] [INFO] Selected 17 target genomes.
[2024-01-24 12:09:43,835] [INFO] Target genome list was writen to GCF_004348345.1_ASM434834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:43,848] [INFO] Task started: fastANI
[2024-01-24 12:09:43,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e8ad705-5ffb-49f0-98e9-19cd8ae1f4fe/GCF_004348345.1_ASM434834v1_genomic.fna.gz --refList GCF_004348345.1_ASM434834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348345.1_ASM434834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:10:26,320] [INFO] Task succeeded: fastANI
[2024-01-24 12:10:26,344] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:10:26,345] [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_004348345.1	s__Nonomuraea longispora	100.0	2795	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	conclusive
GCF_004348685.1	s__Nonomuraea deserti	92.3419	2280	2827	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	85.6436	2032	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645445.1	s__Nonomuraea cypriaca	85.5964	1891	2827	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	85.5749	2007	2827	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	85.5561	1943	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	85.4191	2019	2827	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	85.4132	2024	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.3377	1871	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	85.3293	2049	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	85.2131	1703	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099965.1	s__Nonomuraea jiangxiensis	84.9848	1902	2827	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	84.8909	1780	2827	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	84.8636	1889	2827	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	79.0003	1069	2827	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	78.8599	1072	2827	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	78.7765	1079	2827	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 12:10:26,346] [INFO] GTDB search result was written to GCF_004348345.1_ASM434834v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:10:26,347] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:10:26,350] [INFO] DFAST_QC result json was written to GCF_004348345.1_ASM434834v1_genomic.fna/dqc_result.json
[2024-01-24 12:10:26,351] [INFO] DFAST_QC completed!
[2024-01-24 12:10:26,351] [INFO] Total running time: 0h3m7s