[2024-01-24 12:14:10,621] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,624] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,624] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference
[2024-01-24 12:14:11,918] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,919] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,919] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c34d302-937b-4606-9d02-03d027183a04/GCF_004352805.1_ASM435280v1_genomic.fna.gz | prodigal -d GCF_004352805.1_ASM435280v1_genomic.fna/cds.fna -a GCF_004352805.1_ASM435280v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:39,878] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:39,879] [INFO] Task started: HMMsearch
[2024-01-24 12:14:39,879] [INFO] Running command: hmmsearch --tblout GCF_004352805.1_ASM435280v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/reference_markers.hmm GCF_004352805.1_ASM435280v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:40,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:40,456] [INFO] Found 6/6 markers.
[2024-01-24 12:14:40,536] [INFO] Query marker FASTA was written to GCF_004352805.1_ASM435280v1_genomic.fna/markers.fasta
[2024-01-24 12:14:40,536] [INFO] Task started: Blastn
[2024-01-24 12:14:40,536] [INFO] Running command: blastn -query GCF_004352805.1_ASM435280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/reference_markers.fasta -out GCF_004352805.1_ASM435280v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:41,845] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:41,848] [INFO] Selected 20 target genomes.
[2024-01-24 12:14:41,849] [INFO] Target genome list was writen to GCF_004352805.1_ASM435280v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:41,855] [INFO] Task started: fastANI
[2024-01-24 12:14:41,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c34d302-937b-4606-9d02-03d027183a04/GCF_004352805.1_ASM435280v1_genomic.fna.gz --refList GCF_004352805.1_ASM435280v1_genomic.fna/target_genomes.txt --output GCF_004352805.1_ASM435280v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:26,754] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:26,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:26,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:26,772] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:26,772] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:26,773] [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 mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	100.0	3172	3185	95	conclusive
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	94.9695	2446	3185	95	below_threshold
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	92.1376	2504	3185	95	below_threshold
Nonomuraea diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	91.841	2480	3185	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.6029	1956	3185	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.491	2116	3185	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.4264	2127	3185	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.4149	2201	3185	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.4083	2223	3185	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.2609	2223	3185	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.1192	2044	3185	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.0704	1776	3185	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	84.8935	1906	3185	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.4219	1166	3185	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.005	1845	3185	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	78.9177	1148	3185	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	75.0122	115	3185	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	74.7969	212	3185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:26,775] [INFO] DFAST Taxonomy check result was written to GCF_004352805.1_ASM435280v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:26,776] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:26,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:26,777] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/checkm_data
[2024-01-24 12:15:26,778] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:26,874] [INFO] Task started: CheckM
[2024-01-24 12:15:26,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004352805.1_ASM435280v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004352805.1_ASM435280v1_genomic.fna/checkm_input GCF_004352805.1_ASM435280v1_genomic.fna/checkm_result
[2024-01-24 12:16:59,508] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:59,509] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.15%
Strain heterogeneity: 58.33%
--------------------------------------------------------------------------------
[2024-01-24 12:16:59,540] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:59,541] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:59,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004352805.1_ASM435280v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:59,541] [INFO] Task started: Blastn
[2024-01-24 12:16:59,542] [INFO] Running command: blastn -query GCF_004352805.1_ASM435280v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0de6465-3670-4753-9128-d10d2ff15b17/dqc_reference/reference_markers_gtdb.fasta -out GCF_004352805.1_ASM435280v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:01,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:01,507] [INFO] Selected 23 target genomes.
[2024-01-24 12:17:01,508] [INFO] Target genome list was writen to GCF_004352805.1_ASM435280v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:01,526] [INFO] Task started: fastANI
[2024-01-24 12:17:01,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c34d302-937b-4606-9d02-03d027183a04/GCF_004352805.1_ASM435280v1_genomic.fna.gz --refList GCF_004352805.1_ASM435280v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004352805.1_ASM435280v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:52,872] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:52,893] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:52,893] [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	94.9695	2446	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_004348685.1	s__Nonomuraea deserti	92.136	2504	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_015645445.1	s__Nonomuraea cypriaca	85.5333	1970	3185	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	85.4541	2082	3185	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	85.4534	2173	3185	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	85.4264	2217	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	85.3811	2207	3185	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	85.248	2227	3185	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	85.1664	2036	3185	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	85.0656	1777	3185	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	84.9425	2028	3185	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	84.9366	1898	3185	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	84.9124	2006	3185	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	84.7631	2012	3185	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	83.444	1769	3185	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	79.0462	1142	3185	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	78.9284	1145	3185	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	78.5783	1160	3185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748355.1	s__GCA-2748355 sp002748355	74.8825	51	3185	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__GCA-002748355;g__GCA-2748355	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	74.7965	212	3185	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	74.782	259	3185	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCA_006226595.1	s__M1803 sp006226595	74.733	264	3185	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223645.1	s__QHVT01 sp003223645	74.5704	131	3185	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Gp7-AA8;f__Gp7-AA8;g__QHVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:52,896] [INFO] GTDB search result was written to GCF_004352805.1_ASM435280v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:52,897] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:52,902] [INFO] DFAST_QC result json was written to GCF_004352805.1_ASM435280v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:52,902] [INFO] DFAST_QC completed!
[2024-01-24 12:17:52,902] [INFO] Total running time: 0h3m42s