[2024-01-24 13:09:49,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference
[2024-01-24 13:09:50,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,559] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e04357d-b1c9-4936-8ade-b32b802a790c/GCF_000421565.1_ASM42156v1_genomic.fna.gz | prodigal -d GCF_000421565.1_ASM42156v1_genomic.fna/cds.fna -a GCF_000421565.1_ASM42156v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:03,049] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:03,050] [INFO] Task started: HMMsearch
[2024-01-24 13:10:03,050] [INFO] Running command: hmmsearch --tblout GCF_000421565.1_ASM42156v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/reference_markers.hmm GCF_000421565.1_ASM42156v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:03,353] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:03,355] [INFO] Found 6/6 markers.
[2024-01-24 13:10:03,397] [INFO] Query marker FASTA was written to GCF_000421565.1_ASM42156v1_genomic.fna/markers.fasta
[2024-01-24 13:10:03,397] [INFO] Task started: Blastn
[2024-01-24 13:10:03,397] [INFO] Running command: blastn -query GCF_000421565.1_ASM42156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/reference_markers.fasta -out GCF_000421565.1_ASM42156v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:04,504] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:04,508] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:04,508] [INFO] Target genome list was writen to GCF_000421565.1_ASM42156v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:04,521] [INFO] Task started: fastANI
[2024-01-24 13:10:04,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e04357d-b1c9-4936-8ade-b32b802a790c/GCF_000421565.1_ASM42156v1_genomic.fna.gz --refList GCF_000421565.1_ASM42156v1_genomic.fna/target_genomes.txt --output GCF_000421565.1_ASM42156v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:17,894] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:17,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:17,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:17,912] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:17,912] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:17,912] [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 subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	100.0	1417	1417	95	conclusive
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	86.3067	942	1417	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	86.0784	946	1417	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	86.0498	824	1417	95	below_threshold
Agromyces cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	85.8774	963	1417	95	below_threshold
Agromyces laixinhei	strain=HY052	GCA_006337065.1	2585717	2585717	type	True	84.7916	807	1417	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.3594	584	1417	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.094	851	1417	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	83.0913	806	1417	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	83.0629	866	1417	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.0445	843	1417	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.0271	863	1417	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.7689	612	1417	95	below_threshold
Cryobacterium arcticum	strain=SK-1	GCA_003185895.1	670052	670052	type	True	78.4855	438	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:17,914] [INFO] DFAST Taxonomy check result was written to GCF_000421565.1_ASM42156v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:17,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:17,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:17,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/checkm_data
[2024-01-24 13:10:17,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:17,956] [INFO] Task started: CheckM
[2024-01-24 13:10:17,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421565.1_ASM42156v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421565.1_ASM42156v1_genomic.fna/checkm_input GCF_000421565.1_ASM42156v1_genomic.fna/checkm_result
[2024-01-24 13:11:22,171] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:22,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:22,195] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:22,195] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:22,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421565.1_ASM42156v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:22,196] [INFO] Task started: Blastn
[2024-01-24 13:11:22,196] [INFO] Running command: blastn -query GCF_000421565.1_ASM42156v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7149beef-00ea-47f8-9f23-7a17f067a8d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421565.1_ASM42156v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:24,045] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:24,049] [INFO] Selected 11 target genomes.
[2024-01-24 13:11:24,049] [INFO] Target genome list was writen to GCF_000421565.1_ASM42156v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:24,205] [INFO] Task started: fastANI
[2024-01-24 13:11:24,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e04357d-b1c9-4936-8ade-b32b802a790c/GCF_000421565.1_ASM42156v1_genomic.fna.gz --refList GCF_000421565.1_ASM42156v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421565.1_ASM42156v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:35,173] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:35,193] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:35,193] [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_000421565.1	s__Agromyces subbeticus	100.0	1417	1417	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_004134865.1	s__Agromyces fucosus	86.2767	945	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_013410355.1	s__Agromyces hippuratus	86.0765	946	1417	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	86.0502	824	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_016907835.1	s__Agromyces cerinus_A	86.028	944	1417	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	86.001	887	1417	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	85.8917	962	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337065.1	s__Agromyces laixinhei	84.8221	804	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	99.09	99.02	0.93	0.92	3	-
GCF_009720255.1	s__Agromyces humi	83.3925	580	1417	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134825.1	s__Agromyces albus	83.2345	825	1417	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	83.0486	868	1417	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 13:11:35,195] [INFO] GTDB search result was written to GCF_000421565.1_ASM42156v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:35,196] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:35,200] [INFO] DFAST_QC result json was written to GCF_000421565.1_ASM42156v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:35,200] [INFO] DFAST_QC completed!
[2024-01-24 13:11:35,200] [INFO] Total running time: 0h1m46s