[2024-01-24 12:14:33,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference
[2024-01-24 12:14:34,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg405d5bd9-fdb2-475c-bb0e-67b31bca1c9a/GCF_013407835.1_ASM1340783v1_genomic.fna.gz | prodigal -d GCF_013407835.1_ASM1340783v1_genomic.fna/cds.fna -a GCF_013407835.1_ASM1340783v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,906] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,906] [INFO] Running command: hmmsearch --tblout GCF_013407835.1_ASM1340783v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/reference_markers.hmm GCF_013407835.1_ASM1340783v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:44,107] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:44,108] [INFO] Found 6/6 markers.
[2024-01-24 12:14:44,138] [INFO] Query marker FASTA was written to GCF_013407835.1_ASM1340783v1_genomic.fna/markers.fasta
[2024-01-24 12:14:44,138] [INFO] Task started: Blastn
[2024-01-24 12:14:44,138] [INFO] Running command: blastn -query GCF_013407835.1_ASM1340783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/reference_markers.fasta -out GCF_013407835.1_ASM1340783v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:45,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:45,227] [INFO] Selected 18 target genomes.
[2024-01-24 12:14:45,228] [INFO] Target genome list was writen to GCF_013407835.1_ASM1340783v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:45,233] [INFO] Task started: fastANI
[2024-01-24 12:14:45,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg405d5bd9-fdb2-475c-bb0e-67b31bca1c9a/GCF_013407835.1_ASM1340783v1_genomic.fna.gz --refList GCF_013407835.1_ASM1340783v1_genomic.fna/target_genomes.txt --output GCF_013407835.1_ASM1340783v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:59,543] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:59,544] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:59,544] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:59,554] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:59,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:59,555] [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 atrinae	strain=DSM 23870	GCA_013407835.1	592376	592376	type	True	100.0	1215	1216	95	conclusive
Agromyces atrinae	strain=DSM 23870	GCA_004134805.1	592376	592376	type	True	99.99	1202	1216	95	conclusive
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	80.9802	621	1216	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	80.9673	411	1216	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	80.8786	455	1216	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	80.8475	597	1216	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	80.7337	636	1216	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	80.6574	602	1216	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	80.5945	591	1216	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	80.5539	606	1216	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	80.4962	585	1216	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	80.4614	602	1216	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	80.4366	610	1216	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	80.4051	601	1216	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	80.3463	528	1216	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	80.3309	623	1216	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.171	518	1216	95	below_threshold
Labedella endophytica	strain=EGI 6500705	GCA_003990045.1	1523160	1523160	type	True	78.8246	453	1216	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:59,556] [INFO] DFAST Taxonomy check result was written to GCF_013407835.1_ASM1340783v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:59,556] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:59,556] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:59,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/checkm_data
[2024-01-24 12:14:59,557] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:59,595] [INFO] Task started: CheckM
[2024-01-24 12:14:59,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407835.1_ASM1340783v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407835.1_ASM1340783v1_genomic.fna/checkm_input GCF_013407835.1_ASM1340783v1_genomic.fna/checkm_result
[2024-01-24 12:15:49,464] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:49,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:49,476] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:49,476] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:49,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407835.1_ASM1340783v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:49,477] [INFO] Task started: Blastn
[2024-01-24 12:15:49,477] [INFO] Running command: blastn -query GCF_013407835.1_ASM1340783v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg667c8580-d729-407b-ba12-98752f3510b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407835.1_ASM1340783v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:51,278] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:51,281] [INFO] Selected 23 target genomes.
[2024-01-24 12:15:51,281] [INFO] Target genome list was writen to GCF_013407835.1_ASM1340783v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:51,293] [INFO] Task started: fastANI
[2024-01-24 12:15:51,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg405d5bd9-fdb2-475c-bb0e-67b31bca1c9a/GCF_013407835.1_ASM1340783v1_genomic.fna.gz --refList GCF_013407835.1_ASM1340783v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407835.1_ASM1340783v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:09,836] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:09,850] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:09,850] [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_013407835.1	s__Agromyces_B atrinae	100.0	1216	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces_B	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_013410355.1	s__Agromyces hippuratus	81.1711	627	1216	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	81.0228	600	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	81.0158	408	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134865.1	s__Agromyces fucosus	80.9481	623	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_003384855.1	s__Agromyces sp003384855	80.9354	639	1216	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	80.886	631	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749405.1	s__Agromyces lapidis	80.8473	597	1216	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	80.8225	668	1216	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	80.8177	460	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	80.6763	641	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749395.1	s__Agromyces salentinus	80.6173	587	1216	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	80.6055	556	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113185.1	s__Agromyces sp900113185	80.5979	658	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	80.5498	595	1216	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	80.4716	588	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009729855.1	s__Agromyces luteolus	80.4318	611	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	80.4176	604	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	80.3925	604	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	80.312	625	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018024495.1	s__WSTA01 sp018024495	80.165	519	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789225.1	s__WSTA01 sp009789225	80.0724	551	1216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__WSTA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	79.9084	595	1216	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 12:16:09,851] [INFO] GTDB search result was written to GCF_013407835.1_ASM1340783v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:09,851] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:09,855] [INFO] DFAST_QC result json was written to GCF_013407835.1_ASM1340783v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:09,855] [INFO] DFAST_QC completed!
[2024-01-24 12:16:09,855] [INFO] Total running time: 0h1m36s