[2024-01-24 13:49:40,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference
[2024-01-24 13:49:41,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,210] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg8403d5c9-c1f4-4014-a9f9-76e84b9bff61/GCF_019396405.1_ASM1939640v1_genomic.fna.gz | prodigal -d GCF_019396405.1_ASM1939640v1_genomic.fna/cds.fna -a GCF_019396405.1_ASM1939640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:53,740] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:53,741] [INFO] Task started: HMMsearch
[2024-01-24 13:49:53,741] [INFO] Running command: hmmsearch --tblout GCF_019396405.1_ASM1939640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/reference_markers.hmm GCF_019396405.1_ASM1939640v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:53,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:53,981] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8403d5c9-c1f4-4014-a9f9-76e84b9bff61/GCF_019396405.1_ASM1939640v1_genomic.fna.gz]
[2024-01-24 13:49:54,026] [INFO] Query marker FASTA was written to GCF_019396405.1_ASM1939640v1_genomic.fna/markers.fasta
[2024-01-24 13:49:54,026] [INFO] Task started: Blastn
[2024-01-24 13:49:54,026] [INFO] Running command: blastn -query GCF_019396405.1_ASM1939640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/reference_markers.fasta -out GCF_019396405.1_ASM1939640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:54,977] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:54,987] [INFO] Selected 12 target genomes.
[2024-01-24 13:49:54,987] [INFO] Target genome list was writen to GCF_019396405.1_ASM1939640v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:54,991] [INFO] Task started: fastANI
[2024-01-24 13:49:54,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg8403d5c9-c1f4-4014-a9f9-76e84b9bff61/GCF_019396405.1_ASM1939640v1_genomic.fna.gz --refList GCF_019396405.1_ASM1939640v1_genomic.fna/target_genomes.txt --output GCF_019396405.1_ASM1939640v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:20,614] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:20,614] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:20,615] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:20,623] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:20,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:20,623] [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 rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	100.0	1676	1696	95	conclusive
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	86.92	1360	1696	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	86.8693	1360	1696	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	84.3003	1289	1696	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	84.2174	1298	1696	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	84.2046	1211	1696	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	84.1824	1205	1696	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	84.101	1211	1696	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	84.0732	1144	1696	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.9042	1227	1696	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	83.725	1225	1696	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	83.7242	1105	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:20,624] [INFO] DFAST Taxonomy check result was written to GCF_019396405.1_ASM1939640v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:20,625] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:20,625] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:20,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/checkm_data
[2024-01-24 13:50:20,626] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:20,680] [INFO] Task started: CheckM
[2024-01-24 13:50:20,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019396405.1_ASM1939640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019396405.1_ASM1939640v1_genomic.fna/checkm_input GCF_019396405.1_ASM1939640v1_genomic.fna/checkm_result
[2024-01-24 13:51:01,957] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:01,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.63%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 13:51:01,976] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:01,976] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:01,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019396405.1_ASM1939640v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:01,977] [INFO] Task started: Blastn
[2024-01-24 13:51:01,977] [INFO] Running command: blastn -query GCF_019396405.1_ASM1939640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a8d1d79-f835-40c6-b1a9-29a451a7a8d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_019396405.1_ASM1939640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:03,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:03,548] [INFO] Selected 14 target genomes.
[2024-01-24 13:51:03,548] [INFO] Target genome list was writen to GCF_019396405.1_ASM1939640v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:03,555] [INFO] Task started: fastANI
[2024-01-24 13:51:03,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg8403d5c9-c1f4-4014-a9f9-76e84b9bff61/GCF_019396405.1_ASM1939640v1_genomic.fna.gz --refList GCF_019396405.1_ASM1939640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019396405.1_ASM1939640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:33,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:33,340] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:51:33,340] [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_018603905.1	s__Nonomuraea sp018603905	86.9586	1377	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	84.3903	1152	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	84.3191	1179	1696	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	84.3096	1288	1696	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	84.2015	1300	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	84.1992	1166	1696	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	84.1938	1282	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	84.1661	1199	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	84.1363	1206	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	84.0378	1148	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	84.0239	1283	1696	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	83.8674	1165	1696	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	83.7119	1107	1696	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	83.6947	1230	1696	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:33,342] [INFO] GTDB search result was written to GCF_019396405.1_ASM1939640v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:33,342] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:33,345] [INFO] DFAST_QC result json was written to GCF_019396405.1_ASM1939640v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:33,345] [INFO] DFAST_QC completed!
[2024-01-24 13:51:33,345] [INFO] Total running time: 0h1m53s