[2024-01-24 12:31:05,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:05,252] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:05,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference
[2024-01-24 12:31:06,577] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:06,578] [INFO] Task started: Prodigal
[2024-01-24 12:31:06,579] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f4b516e-0215-4026-aae3-1e03e9f2978c/GCF_004349015.1_ASM434901v1_genomic.fna.gz | prodigal -d GCF_004349015.1_ASM434901v1_genomic.fna/cds.fna -a GCF_004349015.1_ASM434901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:37,682] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:37,683] [INFO] Task started: HMMsearch
[2024-01-24 12:31:37,683] [INFO] Running command: hmmsearch --tblout GCF_004349015.1_ASM434901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/reference_markers.hmm GCF_004349015.1_ASM434901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:38,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:38,147] [INFO] Found 6/6 markers.
[2024-01-24 12:31:38,231] [INFO] Query marker FASTA was written to GCF_004349015.1_ASM434901v1_genomic.fna/markers.fasta
[2024-01-24 12:31:38,232] [INFO] Task started: Blastn
[2024-01-24 12:31:38,232] [INFO] Running command: blastn -query GCF_004349015.1_ASM434901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/reference_markers.fasta -out GCF_004349015.1_ASM434901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:39,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:39,502] [INFO] Selected 20 target genomes.
[2024-01-24 12:31:39,502] [INFO] Target genome list was writen to GCF_004349015.1_ASM434901v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:39,521] [INFO] Task started: fastANI
[2024-01-24 12:31:39,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4b516e-0215-4026-aae3-1e03e9f2978c/GCF_004349015.1_ASM434901v1_genomic.fna.gz --refList GCF_004349015.1_ASM434901v1_genomic.fna/target_genomes.txt --output GCF_004349015.1_ASM434901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:24,892] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:24,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:24,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:24,910] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:24,910] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:24,910] [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 diastatica	strain=KC712	GCA_004349015.1	1848329	1848329	type	True	100.0	3362	3390	95	conclusive
Nonomuraea deserti	strain=KC310	GCA_004348685.1	1848322	1848322	type	True	94.992	2579	3390	95	below_threshold
Nonomuraea longispora	strain=KC201	GCA_004348345.1	1848320	1848320	type	True	91.9526	2297	3390	95	below_threshold
Nonomuraea mesophila	strain=6K102	GCA_004352805.1	2530382	2530382	type	True	91.7741	2476	3390	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.8445	2057	3390	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.7698	2281	3390	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	85.7631	2166	3390	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.6442	2143	3390	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.6293	2158	3390	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.584	2155	3390	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.3971	2258	3390	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.2415	1985	3390	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.2275	1848	3390	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.5068	1182	3390	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.0184	1944	3390	95	below_threshold
Acrocarpospora catenulata	strain=H8750	GCA_018476525.1	2836182	2836182	type	True	78.7931	1154	3390	95	below_threshold
Deinococcus koreensis	strain=SJW1-2	GCA_002901445.1	2054903	2054903	type	True	74.927	202	3390	95	below_threshold
Deinococcus irradiatisoli	strain=17bor-2	GCA_003173015.1	2202254	2202254	type	True	74.8876	136	3390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:24,913] [INFO] DFAST Taxonomy check result was written to GCF_004349015.1_ASM434901v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:24,914] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:24,914] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:24,914] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/checkm_data
[2024-01-24 12:32:24,915] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:25,014] [INFO] Task started: CheckM
[2024-01-24 12:32:25,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349015.1_ASM434901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349015.1_ASM434901v1_genomic.fna/checkm_input GCF_004349015.1_ASM434901v1_genomic.fna/checkm_result
[2024-01-24 12:34:00,696] [INFO] Task succeeded: CheckM
[2024-01-24 12:34:00,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 11.23%
Strain heterogeneity: 44.44%
--------------------------------------------------------------------------------
[2024-01-24 12:34:00,735] [INFO] ===== Completeness check finished =====
[2024-01-24 12:34:00,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:34:00,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349015.1_ASM434901v1_genomic.fna/markers.fasta)
[2024-01-24 12:34:00,736] [INFO] Task started: Blastn
[2024-01-24 12:34:00,736] [INFO] Running command: blastn -query GCF_004349015.1_ASM434901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bb98859-a681-4c40-91d2-1feba6daaf6f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349015.1_ASM434901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:02,668] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:02,674] [INFO] Selected 22 target genomes.
[2024-01-24 12:34:02,674] [INFO] Target genome list was writen to GCF_004349015.1_ASM434901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:34:02,694] [INFO] Task started: fastANI
[2024-01-24 12:34:02,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f4b516e-0215-4026-aae3-1e03e9f2978c/GCF_004349015.1_ASM434901v1_genomic.fna.gz --refList GCF_004349015.1_ASM434901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349015.1_ASM434901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:34:52,371] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:52,393] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:34:52,393] [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_004348685.1	s__Nonomuraea deserti	94.9637	2582	3390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	95.03	95.03	0.77	0.77	2	-
GCF_004348345.1	s__Nonomuraea longispora	91.9464	2298	3390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	97.23	95.05	0.88	0.87	4	-
GCF_015645445.1	s__Nonomuraea cypriaca	85.8681	2053	3390	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	85.8048	2157	3390	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	85.7434	2287	3390	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	85.7236	2246	3390	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	85.5983	2152	3390	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	85.3824	2260	3390	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	85.3525	2235	3390	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	85.2458	1844	3390	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	85.2131	2134	3390	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	85.194	1994	3390	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	85.1915	2111	3390	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	83.3284	1864	3390	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	78.9612	1148	3390	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	78.7691	1171	3390	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	78.7597	1164	3390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Acrocarpospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	74.9325	200	3390	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	74.8082	250	3390	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	74.6857	274	3390	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:34:52,395] [INFO] GTDB search result was written to GCF_004349015.1_ASM434901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:34:52,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:34:52,400] [INFO] DFAST_QC result json was written to GCF_004349015.1_ASM434901v1_genomic.fna/dqc_result.json
[2024-01-24 12:34:52,400] [INFO] DFAST_QC completed!
[2024-01-24 12:34:52,400] [INFO] Total running time: 0h3m47s