[2023-06-27 06:49:22,645] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:49:22,654] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:49:22,654] [INFO] DQC Reference Directory: /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference
[2023-06-27 06:49:23,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:49:23,969] [INFO] Task started: Prodigal
[2023-06-27 06:49:23,969] [INFO] Running command: gunzip -c /var/lib/cwl/stg21954401-d734-4626-b31e-98d55a5a0b6c/GCA_026708205.1_ASM2670820v1_genomic.fna.gz | prodigal -d GCA_026708205.1_ASM2670820v1_genomic.fna/cds.fna -a GCA_026708205.1_ASM2670820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:49:30,278] [INFO] Task succeeded: Prodigal
[2023-06-27 06:49:30,278] [INFO] Task started: HMMsearch
[2023-06-27 06:49:30,278] [INFO] Running command: hmmsearch --tblout GCA_026708205.1_ASM2670820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/reference_markers.hmm GCA_026708205.1_ASM2670820v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:49:30,537] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:49:30,539] [INFO] Found 6/6 markers.
[2023-06-27 06:49:30,587] [INFO] Query marker FASTA was written to GCA_026708205.1_ASM2670820v1_genomic.fna/markers.fasta
[2023-06-27 06:49:30,587] [INFO] Task started: Blastn
[2023-06-27 06:49:30,588] [INFO] Running command: blastn -query GCA_026708205.1_ASM2670820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/reference_markers.fasta -out GCA_026708205.1_ASM2670820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:49:31,317] [INFO] Task succeeded: Blastn
[2023-06-27 06:49:31,338] [INFO] Selected 25 target genomes.
[2023-06-27 06:49:31,339] [INFO] Target genome list was writen to GCA_026708205.1_ASM2670820v1_genomic.fna/target_genomes.txt
[2023-06-27 06:49:31,347] [INFO] Task started: fastANI
[2023-06-27 06:49:31,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg21954401-d734-4626-b31e-98d55a5a0b6c/GCA_026708205.1_ASM2670820v1_genomic.fna.gz --refList GCA_026708205.1_ASM2670820v1_genomic.fna/target_genomes.txt --output GCA_026708205.1_ASM2670820v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:49:46,682] [INFO] Task succeeded: fastANI
[2023-06-27 06:49:46,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:49:46,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:49:46,688] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:49:46,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:49:46,689] [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
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3163	55	662	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.2367	63	662	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.7451	68	662	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:49:46,691] [INFO] DFAST Taxonomy check result was written to GCA_026708205.1_ASM2670820v1_genomic.fna/tc_result.tsv
[2023-06-27 06:49:46,691] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:49:46,692] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:49:46,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/checkm_data
[2023-06-27 06:49:46,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:49:46,735] [INFO] Task started: CheckM
[2023-06-27 06:49:46,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708205.1_ASM2670820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708205.1_ASM2670820v1_genomic.fna/checkm_input GCA_026708205.1_ASM2670820v1_genomic.fna/checkm_result
[2023-06-27 06:50:11,196] [INFO] Task succeeded: CheckM
[2023-06-27 06:50:11,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:50:11,222] [INFO] ===== Completeness check finished =====
[2023-06-27 06:50:11,223] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:50:11,223] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708205.1_ASM2670820v1_genomic.fna/markers.fasta)
[2023-06-27 06:50:11,224] [INFO] Task started: Blastn
[2023-06-27 06:50:11,224] [INFO] Running command: blastn -query GCA_026708205.1_ASM2670820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg349b49af-d4c2-4969-b1c0-be4f10c169b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708205.1_ASM2670820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:50:12,511] [INFO] Task succeeded: Blastn
[2023-06-27 06:50:12,515] [INFO] Selected 9 target genomes.
[2023-06-27 06:50:12,516] [INFO] Target genome list was writen to GCA_026708205.1_ASM2670820v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:50:12,522] [INFO] Task started: fastANI
[2023-06-27 06:50:12,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg21954401-d734-4626-b31e-98d55a5a0b6c/GCA_026708205.1_ASM2670820v1_genomic.fna.gz --refList GCA_026708205.1_ASM2670820v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708205.1_ASM2670820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:50:18,269] [INFO] Task succeeded: fastANI
[2023-06-27 06:50:18,275] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 06:50:18,275] [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
GCA_009845905.1	s__RKRP01 sp009845905	91.2211	556	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	99.99	99.98	0.99	0.99	3	-
GCA_011523505.1	s__RKRP01 sp011523505	90.7984	559	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009838035.1	s__RKRP01 sp009838035	90.6711	557	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	98.62	97.30	0.94	0.92	3	-
GCA_009844425.1	s__RKRP01 sp009844425	90.1895	523	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	99.98	99.98	0.98	0.98	3	-
GCA_007571315.1	s__RKRP01 sp007571315	79.706	282	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__RKRP01;f__RKRP01;g__RKRP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.46	55	662	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-27 06:50:18,277] [INFO] GTDB search result was written to GCA_026708205.1_ASM2670820v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:50:18,278] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:50:18,289] [INFO] DFAST_QC result json was written to GCA_026708205.1_ASM2670820v1_genomic.fna/dqc_result.json
[2023-06-27 06:50:18,289] [INFO] DFAST_QC completed!
[2023-06-27 06:50:18,289] [INFO] Total running time: 0h0m56s