[2024-01-24 12:21:42,267] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:42,269] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:42,270] [INFO] DQC Reference Directory: /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference
[2024-01-24 12:21:43,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:43,584] [INFO] Task started: Prodigal
[2024-01-24 12:21:43,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg3667c86d-3b86-46f4-a0bb-8b4b7bee4514/GCF_009749375.1_ASM974937v1_genomic.fna.gz | prodigal -d GCF_009749375.1_ASM974937v1_genomic.fna/cds.fna -a GCF_009749375.1_ASM974937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:54,264] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:54,264] [INFO] Task started: HMMsearch
[2024-01-24 12:21:54,264] [INFO] Running command: hmmsearch --tblout GCF_009749375.1_ASM974937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/reference_markers.hmm GCF_009749375.1_ASM974937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:54,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:54,612] [INFO] Found 6/6 markers.
[2024-01-24 12:21:54,665] [INFO] Query marker FASTA was written to GCF_009749375.1_ASM974937v1_genomic.fna/markers.fasta
[2024-01-24 12:21:54,665] [INFO] Task started: Blastn
[2024-01-24 12:21:54,666] [INFO] Running command: blastn -query GCF_009749375.1_ASM974937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/reference_markers.fasta -out GCF_009749375.1_ASM974937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:56,010] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:56,013] [INFO] Selected 15 target genomes.
[2024-01-24 12:21:56,014] [INFO] Target genome list was writen to GCF_009749375.1_ASM974937v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:56,019] [INFO] Task started: fastANI
[2024-01-24 12:21:56,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg3667c86d-3b86-46f4-a0bb-8b4b7bee4514/GCF_009749375.1_ASM974937v1_genomic.fna.gz --refList GCF_009749375.1_ASM974937v1_genomic.fna/target_genomes.txt --output GCF_009749375.1_ASM974937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:10,864] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:10,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:10,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:10,879] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:10,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:10,880] [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 italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	100.0	1229	1230	95	conclusive
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	99.9973	1226	1230	95	conclusive
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	90.4686	967	1230	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	84.2959	849	1230	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	84.0198	841	1230	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	83.9323	844	1230	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.6902	720	1230	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.423	796	1230	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	83.2146	817	1230	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.209	793	1230	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	83.0644	766	1230	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.0088	771	1230	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	82.3038	677	1230	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.7809	702	1230	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.9648	627	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:10,882] [INFO] DFAST Taxonomy check result was written to GCF_009749375.1_ASM974937v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:10,883] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:10,883] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:10,883] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/checkm_data
[2024-01-24 12:22:10,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:10,938] [INFO] Task started: CheckM
[2024-01-24 12:22:10,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009749375.1_ASM974937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009749375.1_ASM974937v1_genomic.fna/checkm_input GCF_009749375.1_ASM974937v1_genomic.fna/checkm_result
[2024-01-24 12:23:06,573] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:06,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,605] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:06,606] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:06,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009749375.1_ASM974937v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:06,607] [INFO] Task started: Blastn
[2024-01-24 12:23:06,607] [INFO] Running command: blastn -query GCF_009749375.1_ASM974937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga040e379-5a8a-4812-81e3-8b45880705d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_009749375.1_ASM974937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:08,783] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:08,788] [INFO] Selected 13 target genomes.
[2024-01-24 12:23:08,788] [INFO] Target genome list was writen to GCF_009749375.1_ASM974937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:08,799] [INFO] Task started: fastANI
[2024-01-24 12:23:08,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg3667c86d-3b86-46f4-a0bb-8b4b7bee4514/GCF_009749375.1_ASM974937v1_genomic.fna.gz --refList GCF_009749375.1_ASM974937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009749375.1_ASM974937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:21,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:21,521] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:21,521] [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_000421545.1	s__Agromyces italicus	99.9973	1226	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009749405.1	s__Agromyces lapidis	90.4109	972	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410355.1	s__Agromyces hippuratus	84.2865	851	1230	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	84.1383	792	1230	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	84.0996	860	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142065.1	s__Agromyces cerinus	84.0541	838	1230	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	83.9332	844	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_003070885.1	s__Agromyces badenianii	83.6425	724	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_900113185.1	s__Agromyces sp900113185	83.1575	800	1230	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	83.113	761	1230	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	83.0039	543	1230	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	82.405	774	1230	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645655.1	s__Agromyces bauzanensis	82.3277	675	1230	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 12:23:21,524] [INFO] GTDB search result was written to GCF_009749375.1_ASM974937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:21,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:21,528] [INFO] DFAST_QC result json was written to GCF_009749375.1_ASM974937v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:21,528] [INFO] DFAST_QC completed!
[2024-01-24 12:23:21,528] [INFO] Total running time: 0h1m39s