[2024-01-25 19:56:05,452] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,454] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference
[2024-01-25 19:56:06,607] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,607] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,608] [INFO] Running command: gunzip -c /var/lib/cwl/stg4fdae24d-3085-43d4-814c-4cba7805ebce/GCF_000421545.1_ASM42154v1_genomic.fna.gz | prodigal -d GCF_000421545.1_ASM42154v1_genomic.fna/cds.fna -a GCF_000421545.1_ASM42154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:15,928] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:15,929] [INFO] Task started: HMMsearch
[2024-01-25 19:56:15,929] [INFO] Running command: hmmsearch --tblout GCF_000421545.1_ASM42154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/reference_markers.hmm GCF_000421545.1_ASM42154v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:16,195] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:16,196] [INFO] Found 6/6 markers.
[2024-01-25 19:56:16,230] [INFO] Query marker FASTA was written to GCF_000421545.1_ASM42154v1_genomic.fna/markers.fasta
[2024-01-25 19:56:16,230] [INFO] Task started: Blastn
[2024-01-25 19:56:16,230] [INFO] Running command: blastn -query GCF_000421545.1_ASM42154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/reference_markers.fasta -out GCF_000421545.1_ASM42154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:17,512] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:17,515] [INFO] Selected 15 target genomes.
[2024-01-25 19:56:17,515] [INFO] Target genome list was writen to GCF_000421545.1_ASM42154v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:17,526] [INFO] Task started: fastANI
[2024-01-25 19:56:17,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fdae24d-3085-43d4-814c-4cba7805ebce/GCF_000421545.1_ASM42154v1_genomic.fna.gz --refList GCF_000421545.1_ASM42154v1_genomic.fna/target_genomes.txt --output GCF_000421545.1_ASM42154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:33,315] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:33,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:33,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:33,325] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:56:33,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:33,326] [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=DSM 16388	GCA_000421545.1	279572	279572	type	True	100.0	1237	1237	95	conclusive
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	99.9966	1229	1237	95	conclusive
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	90.5376	972	1237	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	84.3118	856	1237	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	84.0068	845	1237	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	83.9961	851	1237	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.8381	699	1237	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.4779	794	1237	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.3123	779	1237	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	83.2074	818	1237	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	83.1579	768	1237	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	82.9557	786	1237	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	82.3588	683	1237	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.6287	719	1237	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.938	628	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:33,327] [INFO] DFAST Taxonomy check result was written to GCF_000421545.1_ASM42154v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:33,327] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:33,327] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:33,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/checkm_data
[2024-01-25 19:56:33,328] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:33,366] [INFO] Task started: CheckM
[2024-01-25 19:56:33,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421545.1_ASM42154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421545.1_ASM42154v1_genomic.fna/checkm_input GCF_000421545.1_ASM42154v1_genomic.fna/checkm_result
[2024-01-25 19:57:25,056] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:25,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:25,077] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:25,077] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:25,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421545.1_ASM42154v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:25,078] [INFO] Task started: Blastn
[2024-01-25 19:57:25,078] [INFO] Running command: blastn -query GCF_000421545.1_ASM42154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b0a6b10-b8c1-4098-a5fe-c4935e928444/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421545.1_ASM42154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:27,158] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:27,161] [INFO] Selected 13 target genomes.
[2024-01-25 19:57:27,161] [INFO] Target genome list was writen to GCF_000421545.1_ASM42154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:27,186] [INFO] Task started: fastANI
[2024-01-25 19:57:27,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fdae24d-3085-43d4-814c-4cba7805ebce/GCF_000421545.1_ASM42154v1_genomic.fna.gz --refList GCF_000421545.1_ASM42154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421545.1_ASM42154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:40,349] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:40,358] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:40,358] [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	100.0	1237	1237	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	90.554	971	1237	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	84.2883	855	1237	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	84.12	855	1237	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	84.118	795	1237	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	84.0513	845	1237	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	83.9895	846	1237	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	83.8251	700	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_014648575.1	s__Agromyces mediolanus	83.1918	765	1237	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	83.0307	811	1237	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	82.9815	532	1237	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	82.6147	782	1237	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	82.3593	682	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:40,359] [INFO] GTDB search result was written to GCF_000421545.1_ASM42154v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:40,360] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:40,363] [INFO] DFAST_QC result json was written to GCF_000421545.1_ASM42154v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:40,363] [INFO] DFAST_QC completed!
[2024-01-25 19:57:40,363] [INFO] Total running time: 0h1m35s