[2024-01-24 11:05:03,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference
[2024-01-24 11:05:05,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,813] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,814] [INFO] Running command: gunzip -c /var/lib/cwl/stg8175e0e6-da57-49c6-ab31-776aa5ef94b4/GCF_014645655.1_ASM1464565v1_genomic.fna.gz | prodigal -d GCF_014645655.1_ASM1464565v1_genomic.fna/cds.fna -a GCF_014645655.1_ASM1464565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:15,501] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:15,502] [INFO] Task started: HMMsearch
[2024-01-24 11:05:15,502] [INFO] Running command: hmmsearch --tblout GCF_014645655.1_ASM1464565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/reference_markers.hmm GCF_014645655.1_ASM1464565v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:15,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:15,767] [INFO] Found 6/6 markers.
[2024-01-24 11:05:15,805] [INFO] Query marker FASTA was written to GCF_014645655.1_ASM1464565v1_genomic.fna/markers.fasta
[2024-01-24 11:05:15,806] [INFO] Task started: Blastn
[2024-01-24 11:05:15,806] [INFO] Running command: blastn -query GCF_014645655.1_ASM1464565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/reference_markers.fasta -out GCF_014645655.1_ASM1464565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:16,952] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:16,955] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:16,955] [INFO] Target genome list was writen to GCF_014645655.1_ASM1464565v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:16,975] [INFO] Task started: fastANI
[2024-01-24 11:05:16,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg8175e0e6-da57-49c6-ab31-776aa5ef94b4/GCF_014645655.1_ASM1464565v1_genomic.fna.gz --refList GCF_014645655.1_ASM1464565v1_genomic.fna/target_genomes.txt --output GCF_014645655.1_ASM1464565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:32,994] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:32,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:32,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:33,005] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:33,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:33,006] [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 bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	100.0	1200	1205	95	conclusive
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	84.347	797	1205	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	84.2287	788	1205	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.9876	540	1205	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	83.5047	754	1205	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	83.1283	719	1205	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	83.0642	732	1205	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	82.8084	689	1205	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	82.8051	735	1205	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	82.7566	735	1205	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	82.6925	731	1205	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	82.6308	727	1205	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	82.5716	726	1205	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	82.4074	694	1205	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	82.401	724	1205	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.1582	705	1205	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.0224	690	1205	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:33,007] [INFO] DFAST Taxonomy check result was written to GCF_014645655.1_ASM1464565v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:33,008] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:33,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:33,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/checkm_data
[2024-01-24 11:05:33,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:33,047] [INFO] Task started: CheckM
[2024-01-24 11:05:33,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014645655.1_ASM1464565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014645655.1_ASM1464565v1_genomic.fna/checkm_input GCF_014645655.1_ASM1464565v1_genomic.fna/checkm_result
[2024-01-24 11:06:24,694] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:24,695] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:24,710] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:24,710] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:24,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014645655.1_ASM1464565v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:24,710] [INFO] Task started: Blastn
[2024-01-24 11:06:24,710] [INFO] Running command: blastn -query GCF_014645655.1_ASM1464565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaea904fc-b4ed-4c15-8596-cf99a572de65/dqc_reference/reference_markers_gtdb.fasta -out GCF_014645655.1_ASM1464565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:26,648] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:26,651] [INFO] Selected 11 target genomes.
[2024-01-24 11:06:26,651] [INFO] Target genome list was writen to GCF_014645655.1_ASM1464565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:26,657] [INFO] Task started: fastANI
[2024-01-24 11:06:26,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg8175e0e6-da57-49c6-ab31-776aa5ef94b4/GCF_014645655.1_ASM1464565v1_genomic.fna.gz --refList GCF_014645655.1_ASM1464565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014645655.1_ASM1464565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:37,456] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:37,463] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:37,463] [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_014645655.1	s__Agromyces bauzanensis	100.0	1200	1205	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_004959775.1	s__Agromyces sp004959775	89.3062	897	1205	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	87.0805	907	1205	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	84.298	801	1205	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	84.2164	816	1205	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	84.1828	792	1205	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	83.9527	542	1205	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134825.1	s__Agromyces albus	83.0373	735	1205	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	82.9758	709	1205	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907835.1	s__Agromyces cerinus_A	82.968	719	1205	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	82.6608	724	1205	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 11:06:37,465] [INFO] GTDB search result was written to GCF_014645655.1_ASM1464565v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:37,465] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:37,468] [INFO] DFAST_QC result json was written to GCF_014645655.1_ASM1464565v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:37,468] [INFO] DFAST_QC completed!
[2024-01-24 11:06:37,468] [INFO] Total running time: 0h1m34s