[2024-01-24 11:36:20,699] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference
[2024-01-24 11:36:21,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:21,925] [INFO] Task started: Prodigal
[2024-01-24 11:36:21,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg526acc20-eb4f-4d79-a930-3665f51aab28/GCF_027921825.1_ASM2792182v1_genomic.fna.gz | prodigal -d GCF_027921825.1_ASM2792182v1_genomic.fna/cds.fna -a GCF_027921825.1_ASM2792182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:32,251] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:32,252] [INFO] Task started: HMMsearch
[2024-01-24 11:36:32,252] [INFO] Running command: hmmsearch --tblout GCF_027921825.1_ASM2792182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/reference_markers.hmm GCF_027921825.1_ASM2792182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:32,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:32,523] [INFO] Found 6/6 markers.
[2024-01-24 11:36:32,558] [INFO] Query marker FASTA was written to GCF_027921825.1_ASM2792182v1_genomic.fna/markers.fasta
[2024-01-24 11:36:32,558] [INFO] Task started: Blastn
[2024-01-24 11:36:32,558] [INFO] Running command: blastn -query GCF_027921825.1_ASM2792182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/reference_markers.fasta -out GCF_027921825.1_ASM2792182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:33,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:33,979] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:33,980] [INFO] Target genome list was writen to GCF_027921825.1_ASM2792182v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:34,049] [INFO] Task started: fastANI
[2024-01-24 11:36:34,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg526acc20-eb4f-4d79-a930-3665f51aab28/GCF_027921825.1_ASM2792182v1_genomic.fna.gz --refList GCF_027921825.1_ASM2792182v1_genomic.fna/target_genomes.txt --output GCF_027921825.1_ASM2792182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:49,959] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:49,960] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:49,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:49,976] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:36:49,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:49,977] [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
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	99.9827	1277	1301	95	conclusive
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.4131	801	1301	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	83.2006	765	1301	95	below_threshold
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	83.1897	776	1301	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	82.762	747	1301	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	82.5844	767	1301	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	82.521	513	1301	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.4679	747	1301	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	82.3892	717	1301	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	82.345	721	1301	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	82.1088	748	1301	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	82.0962	671	1301	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	81.9524	723	1301	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.9243	687	1301	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	81.9179	692	1301	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	81.837	720	1301	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	81.5197	623	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:49,979] [INFO] DFAST Taxonomy check result was written to GCF_027921825.1_ASM2792182v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:49,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:49,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:49,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/checkm_data
[2024-01-24 11:36:49,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:50,024] [INFO] Task started: CheckM
[2024-01-24 11:36:50,025] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921825.1_ASM2792182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921825.1_ASM2792182v1_genomic.fna/checkm_input GCF_027921825.1_ASM2792182v1_genomic.fna/checkm_result
[2024-01-24 11:37:37,481] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:37,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:37,503] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:37,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:37,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921825.1_ASM2792182v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:37,504] [INFO] Task started: Blastn
[2024-01-24 11:37:37,504] [INFO] Running command: blastn -query GCF_027921825.1_ASM2792182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1279462-5c5a-4351-bdf8-56068ecd2c8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921825.1_ASM2792182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:40,016] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:40,021] [INFO] Selected 18 target genomes.
[2024-01-24 11:37:40,021] [INFO] Target genome list was writen to GCF_027921825.1_ASM2792182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:40,054] [INFO] Task started: fastANI
[2024-01-24 11:37:40,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg526acc20-eb4f-4d79-a930-3665f51aab28/GCF_027921825.1_ASM2792182v1_genomic.fna.gz --refList GCF_027921825.1_ASM2792182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921825.1_ASM2792182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:58,047] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:58,066] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:58,066] [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_014648575.1	s__Agromyces mediolanus	99.9827	1277	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009749405.1	s__Agromyces lapidis	83.4617	797	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421545.1	s__Agromyces italicus	83.19	775	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008122505.1	s__Agromyces sp008122505	82.7788	745	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	82.6597	756	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009647605.1	s__Agromyces sp009647605	82.5316	741	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720255.1	s__Agromyces humi	82.5204	513	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710805.1	s__Agromyces tardus	82.3928	716	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	82.3832	637	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421565.1	s__Agromyces sp001421565	82.3652	787	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	82.2993	725	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	82.2297	750	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	82.1737	741	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006235.1	s__Agromyces sp004006235	82.1311	737	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	81.9875	706	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104685.1	s__Agromyces flavus	81.9768	677	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004959775.1	s__Agromyces sp004959775	81.9588	714	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135405.1	s__Agromyces protaetiae	81.8245	720	1301	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:58,068] [INFO] GTDB search result was written to GCF_027921825.1_ASM2792182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:58,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:58,072] [INFO] DFAST_QC result json was written to GCF_027921825.1_ASM2792182v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:58,072] [INFO] DFAST_QC completed!
[2024-01-24 11:37:58,072] [INFO] Total running time: 0h1m37s