[2024-01-24 14:11:46,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:46,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:46,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference
[2024-01-24 14:11:47,454] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:47,455] [INFO] Task started: Prodigal
[2024-01-24 14:11:47,455] [INFO] Running command: gunzip -c /var/lib/cwl/stg394207e6-6a02-479a-b7cd-5312970d5ad6/GCF_004134865.1_ASM413486v1_genomic.fna.gz | prodigal -d GCF_004134865.1_ASM413486v1_genomic.fna/cds.fna -a GCF_004134865.1_ASM413486v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:11:58,901] [INFO] Task succeeded: Prodigal
[2024-01-24 14:11:58,902] [INFO] Task started: HMMsearch
[2024-01-24 14:11:58,902] [INFO] Running command: hmmsearch --tblout GCF_004134865.1_ASM413486v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/reference_markers.hmm GCF_004134865.1_ASM413486v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:11:59,181] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:11:59,182] [INFO] Found 6/6 markers.
[2024-01-24 14:11:59,227] [INFO] Query marker FASTA was written to GCF_004134865.1_ASM413486v1_genomic.fna/markers.fasta
[2024-01-24 14:11:59,228] [INFO] Task started: Blastn
[2024-01-24 14:11:59,228] [INFO] Running command: blastn -query GCF_004134865.1_ASM413486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/reference_markers.fasta -out GCF_004134865.1_ASM413486v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:00,465] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:00,468] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:00,468] [INFO] Target genome list was writen to GCF_004134865.1_ASM413486v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:00,484] [INFO] Task started: fastANI
[2024-01-24 14:12:00,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg394207e6-6a02-479a-b7cd-5312970d5ad6/GCF_004134865.1_ASM413486v1_genomic.fna.gz --refList GCF_004134865.1_ASM413486v1_genomic.fna/target_genomes.txt --output GCF_004134865.1_ASM413486v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:12,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:12,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:12,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:12,708] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:12,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:12,708] [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 fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	100.0	1334	1334	95	conclusive
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	90.4973	1073	1334	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	90.2435	1100	1334	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	86.5693	825	1334	95	below_threshold
Agromyces laixinhei	strain=HY052	GCA_006337065.1	2585717	2585717	type	True	86.398	857	1334	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	86.2083	958	1334	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.4743	858	1334	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.459	868	1334	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.3105	822	1334	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.4714	809	1334	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.0847	747	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:12,710] [INFO] DFAST Taxonomy check result was written to GCF_004134865.1_ASM413486v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:12,710] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:12,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:12,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/checkm_data
[2024-01-24 14:12:12,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:12,752] [INFO] Task started: CheckM
[2024-01-24 14:12:12,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004134865.1_ASM413486v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004134865.1_ASM413486v1_genomic.fna/checkm_input GCF_004134865.1_ASM413486v1_genomic.fna/checkm_result
[2024-01-24 14:13:01,947] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:01,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:01,970] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:01,971] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:01,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004134865.1_ASM413486v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:01,972] [INFO] Task started: Blastn
[2024-01-24 14:13:01,972] [INFO] Running command: blastn -query GCF_004134865.1_ASM413486v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a7f6911-bc07-4f04-8382-2364e0a5a46a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004134865.1_ASM413486v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:04,080] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:04,084] [INFO] Selected 7 target genomes.
[2024-01-24 14:13:04,084] [INFO] Target genome list was writen to GCF_004134865.1_ASM413486v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:04,091] [INFO] Task started: fastANI
[2024-01-24 14:13:04,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg394207e6-6a02-479a-b7cd-5312970d5ad6/GCF_004134865.1_ASM413486v1_genomic.fna.gz --refList GCF_004134865.1_ASM413486v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004134865.1_ASM413486v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:11,735] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:11,745] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:11,746] [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_004134865.1	s__Agromyces fucosus	100.0	1334	1334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	conclusive
GCF_013410355.1	s__Agromyces hippuratus	90.4974	1073	1334	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	90.348	1094	1334	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	90.2293	1101	1334	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	88.8958	1004	1334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070885.1	s__Agromyces badenianii	86.5759	825	1334	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_000421565.1	s__Agromyces subbeticus	86.2009	959	1334	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 14:13:11,747] [INFO] GTDB search result was written to GCF_004134865.1_ASM413486v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:11,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:11,750] [INFO] DFAST_QC result json was written to GCF_004134865.1_ASM413486v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:11,750] [INFO] DFAST_QC completed!
[2024-01-24 14:13:11,751] [INFO] Total running time: 0h1m25s