[2024-01-24 13:25:47,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference
[2024-01-24 13:25:49,093] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:49,093] [INFO] Task started: Prodigal
[2024-01-24 13:25:49,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg7bbf005f-8005-47e4-a7c7-b3719f16a23d/GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/cds.fna -a GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:59,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:59,836] [INFO] Task started: HMMsearch
[2024-01-24 13:25:59,836] [INFO] Running command: hmmsearch --tblout GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/reference_markers.hmm GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:00,114] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:00,115] [INFO] Found 6/6 markers.
[2024-01-24 13:26:00,150] [INFO] Query marker FASTA was written to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:26:00,151] [INFO] Task started: Blastn
[2024-01-24 13:26:00,151] [INFO] Running command: blastn -query GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/reference_markers.fasta -out GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:01,479] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:01,483] [INFO] Selected 11 target genomes.
[2024-01-24 13:26:01,483] [INFO] Target genome list was writen to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:26:01,489] [INFO] Task started: fastANI
[2024-01-24 13:26:01,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bbf005f-8005-47e4-a7c7-b3719f16a23d/GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna.gz --refList GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:12,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:12,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:12,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:12,230] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:26:12,230] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:12,230] [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_900104685.1	589382	589382	type	True	100.0	1229	1230	95	conclusive
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	99.9959	1216	1230	95	conclusive
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	99.9939	1215	1230	95	conclusive
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	86.7514	998	1230	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	85.0023	918	1230	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	84.9386	909	1230	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	84.9218	589	1230	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	83.7439	788	1230	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.7249	844	1230	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.2934	737	1230	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.9113	572	1230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:12,232] [INFO] DFAST Taxonomy check result was written to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:12,233] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:12,233] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:12,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/checkm_data
[2024-01-24 13:26:12,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:12,276] [INFO] Task started: CheckM
[2024-01-24 13:26:12,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/checkm_input GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:27:15,690] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:15,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:15,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:15,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:15,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:27:15,712] [INFO] Task started: Blastn
[2024-01-24 13:27:15,713] [INFO] Running command: blastn -query GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a76d404-3683-4d9c-9d72-30d5e2e19112/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:17,780] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:17,783] [INFO] Selected 7 target genomes.
[2024-01-24 13:27:17,783] [INFO] Target genome list was writen to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:17,798] [INFO] Task started: fastANI
[2024-01-24 13:27:17,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg7bbf005f-8005-47e4-a7c7-b3719f16a23d/GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna.gz --refList GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:24,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:24,733] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:24,733] [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	100.0	1230	1230	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	86.7636	997	1230	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	85.0159	858	1230	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	84.9898	920	1230	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	84.9159	911	1230	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	84.8737	592	1230	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	84.3964	886	1230	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 13:27:24,735] [INFO] GTDB search result was written to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:24,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:24,739] [INFO] DFAST_QC result json was written to GCF_900104685.1_IMG-taxon_2634166342_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:27:24,739] [INFO] DFAST_QC completed!
[2024-01-24 13:27:24,739] [INFO] Total running time: 0h1m37s