[2024-01-24 15:02:37,926] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:37,928] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:37,929] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference
[2024-01-24 15:02:39,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:39,363] [INFO] Task started: Prodigal
[2024-01-24 15:02:39,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg88c7b560-a024-4215-9a40-1f6583079fc1/GCF_009749405.1_ASM974940v1_genomic.fna.gz | prodigal -d GCF_009749405.1_ASM974940v1_genomic.fna/cds.fna -a GCF_009749405.1_ASM974940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:50,023] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:50,024] [INFO] Task started: HMMsearch
[2024-01-24 15:02:50,024] [INFO] Running command: hmmsearch --tblout GCF_009749405.1_ASM974940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/reference_markers.hmm GCF_009749405.1_ASM974940v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:50,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:50,298] [INFO] Found 6/6 markers.
[2024-01-24 15:02:50,333] [INFO] Query marker FASTA was written to GCF_009749405.1_ASM974940v1_genomic.fna/markers.fasta
[2024-01-24 15:02:50,333] [INFO] Task started: Blastn
[2024-01-24 15:02:50,334] [INFO] Running command: blastn -query GCF_009749405.1_ASM974940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/reference_markers.fasta -out GCF_009749405.1_ASM974940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,697] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,702] [INFO] Selected 14 target genomes.
[2024-01-24 15:02:51,703] [INFO] Target genome list was writen to GCF_009749405.1_ASM974940v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:51,712] [INFO] Task started: fastANI
[2024-01-24 15:02:51,712] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c7b560-a024-4215-9a40-1f6583079fc1/GCF_009749405.1_ASM974940v1_genomic.fna.gz --refList GCF_009749405.1_ASM974940v1_genomic.fna/target_genomes.txt --output GCF_009749405.1_ASM974940v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:06,433] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:06,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:06,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:06,447] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:06,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:06,448] [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 lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	100.0	1258	1258	95	conclusive
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	90.5224	972	1258	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	90.455	977	1258	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	84.9056	901	1258	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	84.7172	908	1258	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	84.5177	902	1258	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	84.078	773	1258	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	84.024	858	1258	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	83.7454	832	1258	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.7166	813	1258	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.5315	823	1258	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	83.4264	806	1258	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.1148	761	1258	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	81.3377	621	1258	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:06,450] [INFO] DFAST Taxonomy check result was written to GCF_009749405.1_ASM974940v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:06,451] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:06,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:06,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/checkm_data
[2024-01-24 15:03:06,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:06,492] [INFO] Task started: CheckM
[2024-01-24 15:03:06,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009749405.1_ASM974940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009749405.1_ASM974940v1_genomic.fna/checkm_input GCF_009749405.1_ASM974940v1_genomic.fna/checkm_result
[2024-01-24 15:04:01,597] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:01,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,619] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:01,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:01,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009749405.1_ASM974940v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:01,621] [INFO] Task started: Blastn
[2024-01-24 15:04:01,621] [INFO] Running command: blastn -query GCF_009749405.1_ASM974940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5612762-edc2-4326-bbd8-15d2c9ead88f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009749405.1_ASM974940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:04,012] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:04,020] [INFO] Selected 13 target genomes.
[2024-01-24 15:04:04,021] [INFO] Target genome list was writen to GCF_009749405.1_ASM974940v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:04,030] [INFO] Task started: fastANI
[2024-01-24 15:04:04,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg88c7b560-a024-4215-9a40-1f6583079fc1/GCF_009749405.1_ASM974940v1_genomic.fna.gz --refList GCF_009749405.1_ASM974940v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009749405.1_ASM974940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:18,835] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:18,853] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:18,854] [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_009749405.1	s__Agromyces lapidis	100.0	1258	1258	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_000421545.1	s__Agromyces italicus	90.5061	973	1258	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410355.1	s__Agromyces hippuratus	84.8511	906	1258	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	84.7203	907	1258	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	84.6855	866	1258	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	84.6699	929	1258	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	84.5258	901	1258	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	84.0687	774	1258	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	83.5037	884	1258	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	83.4171	807	1258	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	82.9013	817	1258	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	82.8683	762	1258	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	82.777	733	1258	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 15:04:18,857] [INFO] GTDB search result was written to GCF_009749405.1_ASM974940v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:18,857] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:18,861] [INFO] DFAST_QC result json was written to GCF_009749405.1_ASM974940v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:18,862] [INFO] DFAST_QC completed!
[2024-01-24 15:04:18,862] [INFO] Total running time: 0h1m41s