[2024-01-25 18:12:05,526] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:05,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:05,527] [INFO] DQC Reference Directory: /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference
[2024-01-25 18:12:06,666] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:06,667] [INFO] Task started: Prodigal
[2024-01-25 18:12:06,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bdb2f10-235d-4fab-887f-dfdc093f62a2/GCF_009749385.1_ASM974938v1_genomic.fna.gz | prodigal -d GCF_009749385.1_ASM974938v1_genomic.fna/cds.fna -a GCF_009749385.1_ASM974938v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:17,483] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:17,483] [INFO] Task started: HMMsearch
[2024-01-25 18:12:17,483] [INFO] Running command: hmmsearch --tblout GCF_009749385.1_ASM974938v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/reference_markers.hmm GCF_009749385.1_ASM974938v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:17,700] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:17,701] [INFO] Found 6/6 markers.
[2024-01-25 18:12:17,741] [INFO] Query marker FASTA was written to GCF_009749385.1_ASM974938v1_genomic.fna/markers.fasta
[2024-01-25 18:12:17,741] [INFO] Task started: Blastn
[2024-01-25 18:12:17,741] [INFO] Running command: blastn -query GCF_009749385.1_ASM974938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/reference_markers.fasta -out GCF_009749385.1_ASM974938v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:18,936] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:18,939] [INFO] Selected 15 target genomes.
[2024-01-25 18:12:18,939] [INFO] Target genome list was writen to GCF_009749385.1_ASM974938v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:18,943] [INFO] Task started: fastANI
[2024-01-25 18:12:18,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bdb2f10-235d-4fab-887f-dfdc093f62a2/GCF_009749385.1_ASM974938v1_genomic.fna.gz --refList GCF_009749385.1_ASM974938v1_genomic.fna/target_genomes.txt --output GCF_009749385.1_ASM974938v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:35,585] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:35,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:35,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:35,600] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:35,600] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:35,601] [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 allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	100.0	1441	1441	95	conclusive
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	91.313	1146	1441	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	86.4507	962	1441	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	85.653	961	1441	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	83.6932	855	1441	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.6657	845	1441	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.66	596	1441	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	83.5518	880	1441	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.4378	880	1441	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.3327	749	1441	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	83.2724	842	1441	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.867	833	1441	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	82.8336	817	1441	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	82.6391	806	1441	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.9286	659	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:35,602] [INFO] DFAST Taxonomy check result was written to GCF_009749385.1_ASM974938v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:35,602] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:35,603] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:35,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/checkm_data
[2024-01-25 18:12:35,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:35,644] [INFO] Task started: CheckM
[2024-01-25 18:12:35,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009749385.1_ASM974938v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009749385.1_ASM974938v1_genomic.fna/checkm_input GCF_009749385.1_ASM974938v1_genomic.fna/checkm_result
[2024-01-25 18:13:44,034] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:44,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:44,052] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:44,053] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:44,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009749385.1_ASM974938v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:44,054] [INFO] Task started: Blastn
[2024-01-25 18:13:44,054] [INFO] Running command: blastn -query GCF_009749385.1_ASM974938v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56e5f3cc-9421-4970-9baa-e22b63cbbc06/dqc_reference/reference_markers_gtdb.fasta -out GCF_009749385.1_ASM974938v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:46,087] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:46,089] [INFO] Selected 6 target genomes.
[2024-01-25 18:13:46,090] [INFO] Target genome list was writen to GCF_009749385.1_ASM974938v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:46,105] [INFO] Task started: fastANI
[2024-01-25 18:13:46,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bdb2f10-235d-4fab-887f-dfdc093f62a2/GCF_009749385.1_ASM974938v1_genomic.fna.gz --refList GCF_009749385.1_ASM974938v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009749385.1_ASM974938v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:53,851] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:53,856] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:53,856] [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_009749385.1	s__Agromyces allii	100.0	1441	1441	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_001660485.1	s__Agromyces aureus	91.3278	1145	1441	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001421565.1	s__Agromyces sp001421565	89.5256	1169	1441	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	89.3794	1150	1441	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	89.3467	1114	1441	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749465.1	s__Agromyces terreus	86.4527	962	1441	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 18:13:53,858] [INFO] GTDB search result was written to GCF_009749385.1_ASM974938v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:53,858] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:53,861] [INFO] DFAST_QC result json was written to GCF_009749385.1_ASM974938v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:53,861] [INFO] DFAST_QC completed!
[2024-01-25 18:13:53,861] [INFO] Total running time: 0h1m48s