[2024-01-24 13:28:25,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,513] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference
[2024-01-24 13:28:26,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:26,832] [INFO] Task started: Prodigal
[2024-01-24 13:28:26,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg49908d1b-aa37-4dd0-ae50-3b3e8fb62c26/GCF_007923295.1_ASM792329v1_genomic.fna.gz | prodigal -d GCF_007923295.1_ASM792329v1_genomic.fna/cds.fna -a GCF_007923295.1_ASM792329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:34,839] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:34,839] [INFO] Task started: HMMsearch
[2024-01-24 13:28:34,839] [INFO] Running command: hmmsearch --tblout GCF_007923295.1_ASM792329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/reference_markers.hmm GCF_007923295.1_ASM792329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,123] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,124] [INFO] Found 6/6 markers.
[2024-01-24 13:28:35,158] [INFO] Query marker FASTA was written to GCF_007923295.1_ASM792329v1_genomic.fna/markers.fasta
[2024-01-24 13:28:35,159] [INFO] Task started: Blastn
[2024-01-24 13:28:35,159] [INFO] Running command: blastn -query GCF_007923295.1_ASM792329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/reference_markers.fasta -out GCF_007923295.1_ASM792329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:36,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:36,649] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:36,650] [INFO] Target genome list was writen to GCF_007923295.1_ASM792329v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:36,655] [INFO] Task started: fastANI
[2024-01-24 13:28:36,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg49908d1b-aa37-4dd0-ae50-3b3e8fb62c26/GCF_007923295.1_ASM792329v1_genomic.fna.gz --refList GCF_007923295.1_ASM792329v1_genomic.fna/target_genomes.txt --output GCF_007923295.1_ASM792329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:46,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:46,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:46,176] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:46,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:46,177] [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
Agrococcus sediminis	strain=NS18	GCA_007923295.1	2599924	2599924	type	True	100.0	903	904	95	conclusive
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	87.3943	697	904	95	below_threshold
Agrococcus lahaulensis	strain=DSM 17612	GCA_000425105.1	341722	341722	type	True	87.3852	703	904	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	87.2841	717	904	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	86.9415	700	904	95	below_threshold
Agrococcus terreus	strain=CGMCC 1.6960	GCA_014645235.1	574649	574649	type	True	86.2432	696	904	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.7292	467	904	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.7045	459	904	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.6834	398	904	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	78.6591	330	904	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.4413	382	904	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,178] [INFO] DFAST Taxonomy check result was written to GCF_007923295.1_ASM792329v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:46,179] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:46,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:46,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/checkm_data
[2024-01-24 13:28:46,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:46,211] [INFO] Task started: CheckM
[2024-01-24 13:28:46,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007923295.1_ASM792329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007923295.1_ASM792329v1_genomic.fna/checkm_input GCF_007923295.1_ASM792329v1_genomic.fna/checkm_result
[2024-01-24 13:29:25,784] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:25,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:25,801] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:25,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:25,802] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007923295.1_ASM792329v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:25,802] [INFO] Task started: Blastn
[2024-01-24 13:29:25,802] [INFO] Running command: blastn -query GCF_007923295.1_ASM792329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg525d42d1-a9f5-4113-9559-5fadd8122cd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007923295.1_ASM792329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:28,234] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:28,238] [INFO] Selected 10 target genomes.
[2024-01-24 13:29:28,239] [INFO] Target genome list was writen to GCF_007923295.1_ASM792329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:28,251] [INFO] Task started: fastANI
[2024-01-24 13:29:28,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg49908d1b-aa37-4dd0-ae50-3b3e8fb62c26/GCF_007923295.1_ASM792329v1_genomic.fna.gz --refList GCF_007923295.1_ASM792329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007923295.1_ASM792329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:36,944] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:36,962] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:36,963] [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_007923295.1	s__Agrococcus sediminis	100.0	903	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.99	97.99	0.92	0.92	2	conclusive
GCF_000400485.1	s__Agrococcus pavilionensis	87.4592	694	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	97.37	97.37	0.91	0.91	2	-
GCF_018308945.1	s__Agrococcus sp018308945	87.44	676	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425105.1	s__Agrococcus lahaulensis	87.367	704	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752465.1	s__Agrococcus jenensis	87.2593	718	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104705.1	s__Agrococcus carbonis	86.9451	700	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007988785.1	s__Agrococcus baldri_A	86.3638	695	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645235.1	s__Agrococcus terreus	86.2419	696	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017168255.1	s__Agrococcus sp017168255	85.8762	677	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900114805.1	s__Agrococcus baldri	85.6814	686	904	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agrococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:36,965] [INFO] GTDB search result was written to GCF_007923295.1_ASM792329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:36,967] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:36,972] [INFO] DFAST_QC result json was written to GCF_007923295.1_ASM792329v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:36,972] [INFO] DFAST_QC completed!
[2024-01-24 13:29:36,972] [INFO] Total running time: 0h1m11s