[2024-01-25 20:17:50,754] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,756] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference
[2024-01-25 20:17:51,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,901] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg4433a6ed-95b7-4290-afd5-7cfd852b3854/GCF_011090295.1_ASM1109029v1_genomic.fna.gz | prodigal -d GCF_011090295.1_ASM1109029v1_genomic.fna/cds.fna -a GCF_011090295.1_ASM1109029v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:18:15,067] [INFO] Task succeeded: Prodigal
[2024-01-25 20:18:15,068] [INFO] Task started: HMMsearch
[2024-01-25 20:18:15,068] [INFO] Running command: hmmsearch --tblout GCF_011090295.1_ASM1109029v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/reference_markers.hmm GCF_011090295.1_ASM1109029v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:18:15,263] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:18:15,264] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg4433a6ed-95b7-4290-afd5-7cfd852b3854/GCF_011090295.1_ASM1109029v1_genomic.fna.gz]
[2024-01-25 20:18:15,312] [INFO] Query marker FASTA was written to GCF_011090295.1_ASM1109029v1_genomic.fna/markers.fasta
[2024-01-25 20:18:15,313] [INFO] Task started: Blastn
[2024-01-25 20:18:15,313] [INFO] Running command: blastn -query GCF_011090295.1_ASM1109029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/reference_markers.fasta -out GCF_011090295.1_ASM1109029v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:15,854] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:15,857] [INFO] Selected 7 target genomes.
[2024-01-25 20:18:15,857] [INFO] Target genome list was writen to GCF_011090295.1_ASM1109029v1_genomic.fna/target_genomes.txt
[2024-01-25 20:18:15,863] [INFO] Task started: fastANI
[2024-01-25 20:18:15,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg4433a6ed-95b7-4290-afd5-7cfd852b3854/GCF_011090295.1_ASM1109029v1_genomic.fna.gz --refList GCF_011090295.1_ASM1109029v1_genomic.fna/target_genomes.txt --output GCF_011090295.1_ASM1109029v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:25,201] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:25,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:25,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:25,208] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:25,208] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:25,208] [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
Nocardioides aromaticivorans	strain=DSM 15131	GCA_013408525.1	200618	200618	type	True	85.8073	1173	1595	95	below_threshold
Nocardioides kongjuensis	strain=DSM 19082	GCA_013409625.1	349522	349522	type	True	84.6794	1056	1595	95	below_threshold
Nocardioides humi	strain=DCY24	GCA_006494775.1	449461	449461	type	True	84.6432	1059	1595	95	below_threshold
Nocardioides nitrophenolicus	strain=DSM 15529	GCA_016907515.1	60489	60489	type	True	84.5226	1088	1595	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	84.4735	1097	1595	95	below_threshold
Nocardioides daeguensis	strain=2C1-5	GCA_019192965.1	908359	908359	type	True	84.4477	1002	1595	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	84.4063	1101	1595	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:25,209] [INFO] DFAST Taxonomy check result was written to GCF_011090295.1_ASM1109029v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:25,210] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:25,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:25,211] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/checkm_data
[2024-01-25 20:18:25,212] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:25,261] [INFO] Task started: CheckM
[2024-01-25 20:18:25,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011090295.1_ASM1109029v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011090295.1_ASM1109029v1_genomic.fna/checkm_input GCF_011090295.1_ASM1109029v1_genomic.fna/checkm_result
[2024-01-25 20:19:34,880] [INFO] Task succeeded: CheckM
[2024-01-25 20:19:34,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.14%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:19:34,902] [INFO] ===== Completeness check finished =====
[2024-01-25 20:19:34,903] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:19:34,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011090295.1_ASM1109029v1_genomic.fna/markers.fasta)
[2024-01-25 20:19:34,903] [INFO] Task started: Blastn
[2024-01-25 20:19:34,903] [INFO] Running command: blastn -query GCF_011090295.1_ASM1109029v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49aa4c28-54af-4ca6-bc99-ab6e8f65eeba/dqc_reference/reference_markers_gtdb.fasta -out GCF_011090295.1_ASM1109029v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:35,466] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:35,472] [INFO] Selected 9 target genomes.
[2024-01-25 20:19:35,472] [INFO] Target genome list was writen to GCF_011090295.1_ASM1109029v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:19:35,486] [INFO] Task started: fastANI
[2024-01-25 20:19:35,486] [INFO] Running command: fastANI --query /var/lib/cwl/stg4433a6ed-95b7-4290-afd5-7cfd852b3854/GCF_011090295.1_ASM1109029v1_genomic.fna.gz --refList GCF_011090295.1_ASM1109029v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011090295.1_ASM1109029v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:19:47,775] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:47,782] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:19:47,783] [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_013408525.1	s__Nocardioides aromaticivorans	85.8034	1175	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.43	98.36	0.91	0.91	3	-
GCF_003054165.1	s__Nocardioides sp003054165	85.5752	1128	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803235.1	s__Nocardioides simplex_A	84.8047	1046	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409625.1	s__Nocardioides kongjuensis	84.6747	1056	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715725.1	s__Nocardioides sp006715725	84.6034	1081	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907515.1	s__Nocardioides nitrophenolicus	84.5552	1083	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019192965.1	s__Nocardioides daeguensis	84.4851	999	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	84.4682	1120	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114845.1	s__Nocardioides simplex	84.4012	1105	1595	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.16	97.49	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:19:47,784] [INFO] GTDB search result was written to GCF_011090295.1_ASM1109029v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:19:47,785] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:19:47,787] [INFO] DFAST_QC result json was written to GCF_011090295.1_ASM1109029v1_genomic.fna/dqc_result.json
[2024-01-25 20:19:47,787] [INFO] DFAST_QC completed!
[2024-01-25 20:19:47,787] [INFO] Total running time: 0h1m57s