[2024-01-25 19:38:05,931] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:38:05,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:38:05,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference
[2024-01-25 19:38:07,082] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:38:07,083] [INFO] Task started: Prodigal
[2024-01-25 19:38:07,083] [INFO] Running command: gunzip -c /var/lib/cwl/stg654f38ab-62de-4e66-a2bf-7ab50b49eea3/GCF_009749395.1_ASM974939v1_genomic.fna.gz | prodigal -d GCF_009749395.1_ASM974939v1_genomic.fna/cds.fna -a GCF_009749395.1_ASM974939v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:38:17,820] [INFO] Task succeeded: Prodigal
[2024-01-25 19:38:17,821] [INFO] Task started: HMMsearch
[2024-01-25 19:38:17,821] [INFO] Running command: hmmsearch --tblout GCF_009749395.1_ASM974939v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/reference_markers.hmm GCF_009749395.1_ASM974939v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:38:18,040] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:38:18,041] [INFO] Found 6/6 markers.
[2024-01-25 19:38:18,076] [INFO] Query marker FASTA was written to GCF_009749395.1_ASM974939v1_genomic.fna/markers.fasta
[2024-01-25 19:38:18,077] [INFO] Task started: Blastn
[2024-01-25 19:38:18,077] [INFO] Running command: blastn -query GCF_009749395.1_ASM974939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/reference_markers.fasta -out GCF_009749395.1_ASM974939v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:19,286] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:19,288] [INFO] Selected 13 target genomes.
[2024-01-25 19:38:19,289] [INFO] Target genome list was writen to GCF_009749395.1_ASM974939v1_genomic.fna/target_genomes.txt
[2024-01-25 19:38:19,291] [INFO] Task started: fastANI
[2024-01-25 19:38:19,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg654f38ab-62de-4e66-a2bf-7ab50b49eea3/GCF_009749395.1_ASM974939v1_genomic.fna.gz --refList GCF_009749395.1_ASM974939v1_genomic.fna/target_genomes.txt --output GCF_009749395.1_ASM974939v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:38:32,241] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:32,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:38:32,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:38:32,250] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:38:32,250] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:38:32,250] [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 salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	100.0	1379	1390	95	conclusive
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	86.2675	982	1390	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	85.7388	989	1390	95	below_threshold
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	85.469	1008	1390	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.1901	612	1390	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	83.071	827	1390	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.013	849	1390	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	82.9016	718	1390	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	82.7133	803	1390	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.4679	872	1390	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	82.1848	815	1390	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	81.8589	784	1390	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.4842	629	1390	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:38:32,252] [INFO] DFAST Taxonomy check result was written to GCF_009749395.1_ASM974939v1_genomic.fna/tc_result.tsv
[2024-01-25 19:38:32,252] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:38:32,252] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:38:32,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/checkm_data
[2024-01-25 19:38:32,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:38:32,294] [INFO] Task started: CheckM
[2024-01-25 19:38:32,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009749395.1_ASM974939v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009749395.1_ASM974939v1_genomic.fna/checkm_input GCF_009749395.1_ASM974939v1_genomic.fna/checkm_result
[2024-01-25 19:39:35,283] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:35,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:35,300] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:35,300] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:35,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009749395.1_ASM974939v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:35,301] [INFO] Task started: Blastn
[2024-01-25 19:39:35,301] [INFO] Running command: blastn -query GCF_009749395.1_ASM974939v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d9db046-96e1-44ff-96b7-69ee3f4b8b71/dqc_reference/reference_markers_gtdb.fasta -out GCF_009749395.1_ASM974939v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:37,303] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:37,306] [INFO] Selected 7 target genomes.
[2024-01-25 19:39:37,306] [INFO] Target genome list was writen to GCF_009749395.1_ASM974939v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:37,313] [INFO] Task started: fastANI
[2024-01-25 19:39:37,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg654f38ab-62de-4e66-a2bf-7ab50b49eea3/GCF_009749395.1_ASM974939v1_genomic.fna.gz --refList GCF_009749395.1_ASM974939v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009749395.1_ASM974939v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:45,512] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:45,518] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:45,518] [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_009749395.1	s__Agromyces salentinus	100.0	1377	1390	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_001421565.1	s__Agromyces sp001421565	86.357	1077	1390	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	86.2677	982	1390	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	86.1134	1011	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749385.1	s__Agromyces allii	85.7958	984	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660485.1	s__Agromyces aureus	85.4664	1008	1390	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113185.1	s__Agromyces sp900113185	85.2427	982	1390	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 19:39:45,520] [INFO] GTDB search result was written to GCF_009749395.1_ASM974939v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:45,520] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:45,523] [INFO] DFAST_QC result json was written to GCF_009749395.1_ASM974939v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:45,523] [INFO] DFAST_QC completed!
[2024-01-25 19:39:45,523] [INFO] Total running time: 0h1m40s