[2024-01-24 12:44:11,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:11,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:11,034] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference
[2024-01-24 12:44:12,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,402] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d433ff0-5848-46ef-be13-7a5367b77831/GCF_004366335.2_ASM436633v2_genomic.fna.gz | prodigal -d GCF_004366335.2_ASM436633v2_genomic.fna/cds.fna -a GCF_004366335.2_ASM436633v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:23,112] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:23,112] [INFO] Task started: HMMsearch
[2024-01-24 12:44:23,112] [INFO] Running command: hmmsearch --tblout GCF_004366335.2_ASM436633v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/reference_markers.hmm GCF_004366335.2_ASM436633v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:23,433] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:23,434] [INFO] Found 6/6 markers.
[2024-01-24 12:44:23,472] [INFO] Query marker FASTA was written to GCF_004366335.2_ASM436633v2_genomic.fna/markers.fasta
[2024-01-24 12:44:23,472] [INFO] Task started: Blastn
[2024-01-24 12:44:23,472] [INFO] Running command: blastn -query GCF_004366335.2_ASM436633v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/reference_markers.fasta -out GCF_004366335.2_ASM436633v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:24,855] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:24,862] [INFO] Selected 11 target genomes.
[2024-01-24 12:44:24,862] [INFO] Target genome list was writen to GCF_004366335.2_ASM436633v2_genomic.fna/target_genomes.txt
[2024-01-24 12:44:24,872] [INFO] Task started: fastANI
[2024-01-24 12:44:24,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d433ff0-5848-46ef-be13-7a5367b77831/GCF_004366335.2_ASM436633v2_genomic.fna.gz --refList GCF_004366335.2_ASM436633v2_genomic.fna/target_genomes.txt --output GCF_004366335.2_ASM436633v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:35,962] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:35,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:35,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:35,973] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:44:35,973] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:35,974] [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 flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	100.0	1216	1217	95	conclusive
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	99.9995	1211	1217	95	conclusive
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	99.9994	1217	1217	95	conclusive
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	86.8104	993	1217	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	85.0681	920	1217	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	84.8917	591	1217	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	84.8197	912	1217	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.7022	858	1217	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	83.7003	781	1217	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.2027	751	1217	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.5559	592	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:35,975] [INFO] DFAST Taxonomy check result was written to GCF_004366335.2_ASM436633v2_genomic.fna/tc_result.tsv
[2024-01-24 12:44:35,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:35,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:35,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/checkm_data
[2024-01-24 12:44:35,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:36,015] [INFO] Task started: CheckM
[2024-01-24 12:44:36,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004366335.2_ASM436633v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004366335.2_ASM436633v2_genomic.fna/checkm_input GCF_004366335.2_ASM436633v2_genomic.fna/checkm_result
[2024-01-24 12:45:31,241] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:31,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:31,263] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:31,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:31,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004366335.2_ASM436633v2_genomic.fna/markers.fasta)
[2024-01-24 12:45:31,264] [INFO] Task started: Blastn
[2024-01-24 12:45:31,264] [INFO] Running command: blastn -query GCF_004366335.2_ASM436633v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc5e2837-f872-403b-84e9-95b17043b54c/dqc_reference/reference_markers_gtdb.fasta -out GCF_004366335.2_ASM436633v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:33,328] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:33,332] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:33,332] [INFO] Target genome list was writen to GCF_004366335.2_ASM436633v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:33,345] [INFO] Task started: fastANI
[2024-01-24 12:45:33,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d433ff0-5848-46ef-be13-7a5367b77831/GCF_004366335.2_ASM436633v2_genomic.fna.gz --refList GCF_004366335.2_ASM436633v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004366335.2_ASM436633v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:40,179] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:40,187] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:40,188] [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_900104685.1	s__Agromyces flavus	99.9994	1217	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_016907355.1	s__Agromyces aurantiacus	86.8227	992	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	85.0865	918	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	85.0256	858	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	84.9059	590	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	84.831	911	1217	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	84.6285	869	1217	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 12:45:40,190] [INFO] GTDB search result was written to GCF_004366335.2_ASM436633v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:40,191] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:40,195] [INFO] DFAST_QC result json was written to GCF_004366335.2_ASM436633v2_genomic.fna/dqc_result.json
[2024-01-24 12:45:40,195] [INFO] DFAST_QC completed!
[2024-01-24 12:45:40,195] [INFO] Total running time: 0h1m29s