[2023-06-04 19:37:54,406] [INFO] DFAST_QC pipeline started.
[2023-06-04 19:37:54,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 19:37:54,409] [INFO] DQC Reference Directory: /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference
[2023-06-04 19:37:56,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 19:37:56,361] [INFO] Task started: Prodigal
[2023-06-04 19:37:56,361] [INFO] Running command: gunzip -c /var/lib/cwl/stga211691f-cbbd-4abb-b9c4-dae1becaaef1/GCA_001773855.1_ASM177385v1_genomic.fna.gz | prodigal -d GCA_001773855.1_ASM177385v1_genomic.fna/cds.fna -a GCA_001773855.1_ASM177385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 19:38:00,183] [INFO] Task succeeded: Prodigal
[2023-06-04 19:38:00,183] [INFO] Task started: HMMsearch
[2023-06-04 19:38:00,183] [INFO] Running command: hmmsearch --tblout GCA_001773855.1_ASM177385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/reference_markers.hmm GCA_001773855.1_ASM177385v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 19:38:00,385] [INFO] Task succeeded: HMMsearch
[2023-06-04 19:38:00,386] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga211691f-cbbd-4abb-b9c4-dae1becaaef1/GCA_001773855.1_ASM177385v1_genomic.fna.gz]
[2023-06-04 19:38:00,412] [INFO] Query marker FASTA was written to GCA_001773855.1_ASM177385v1_genomic.fna/markers.fasta
[2023-06-04 19:38:00,413] [INFO] Task started: Blastn
[2023-06-04 19:38:00,413] [INFO] Running command: blastn -query GCA_001773855.1_ASM177385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/reference_markers.fasta -out GCA_001773855.1_ASM177385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:01,021] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:01,025] [INFO] Selected 20 target genomes.
[2023-06-04 19:38:01,025] [INFO] Target genome list was writen to GCA_001773855.1_ASM177385v1_genomic.fna/target_genomes.txt
[2023-06-04 19:38:01,243] [INFO] Task started: fastANI
[2023-06-04 19:38:01,244] [INFO] Running command: fastANI --query /var/lib/cwl/stga211691f-cbbd-4abb-b9c4-dae1becaaef1/GCA_001773855.1_ASM177385v1_genomic.fna.gz --refList GCA_001773855.1_ASM177385v1_genomic.fna/target_genomes.txt --output GCA_001773855.1_ASM177385v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 19:38:18,341] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:18,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 19:38:18,342] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 19:38:18,344] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 19:38:18,344] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 19:38:18,344] [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
--------------------------------------------------------------------------------
[2023-06-04 19:38:18,346] [INFO] DFAST Taxonomy check result was written to GCA_001773855.1_ASM177385v1_genomic.fna/tc_result.tsv
[2023-06-04 19:38:18,347] [INFO] ===== Taxonomy check completed =====
[2023-06-04 19:38:18,347] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 19:38:18,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/checkm_data
[2023-06-04 19:38:18,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 19:38:18,375] [INFO] Task started: CheckM
[2023-06-04 19:38:18,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001773855.1_ASM177385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001773855.1_ASM177385v1_genomic.fna/checkm_input GCA_001773855.1_ASM177385v1_genomic.fna/checkm_result
[2023-06-04 19:38:36,200] [INFO] Task succeeded: CheckM
[2023-06-04 19:38:36,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:38:36,223] [INFO] ===== Completeness check finished =====
[2023-06-04 19:38:36,223] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:38:36,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001773855.1_ASM177385v1_genomic.fna/markers.fasta)
[2023-06-04 19:38:36,224] [INFO] Task started: Blastn
[2023-06-04 19:38:36,224] [INFO] Running command: blastn -query GCA_001773855.1_ASM177385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60f0fc31-9a67-4a40-adea-fc7cc4bdc93c/dqc_reference/reference_markers_gtdb.fasta -out GCA_001773855.1_ASM177385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:38:36,756] [INFO] Task succeeded: Blastn
[2023-06-04 19:38:36,761] [INFO] Selected 8 target genomes.
[2023-06-04 19:38:36,761] [INFO] Target genome list was writen to GCA_001773855.1_ASM177385v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:38:36,860] [INFO] Task started: fastANI
[2023-06-04 19:38:36,861] [INFO] Running command: fastANI --query /var/lib/cwl/stga211691f-cbbd-4abb-b9c4-dae1becaaef1/GCA_001773855.1_ASM177385v1_genomic.fna.gz --refList GCA_001773855.1_ASM177385v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001773855.1_ASM177385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:38:40,898] [INFO] Task succeeded: fastANI
[2023-06-04 19:38:40,912] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:38:40,912] [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_001773855.1	s__RBG-16-66-30 sp001773855	100.0	506	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014894455.1	s__RBG-16-66-30 sp014894455	89.9395	392	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001775755.1	s__RBG-16-66-30 sp001775755	85.1415	339	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	99.12	99.12	0.81	0.81	2	-
GCA_001775715.1	s__RBG-16-66-30 sp001775715	84.1781	279	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999365.1	s__RBG-16-66-30 sp012516875	82.1679	321	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	99.63	99.63	0.88	0.88	2	-
GCA_017883305.1	s__RBG-16-66-30 sp017883305	81.838	314	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011048485.1	s__RBG-16-66-30 sp011048485	80.5977	179	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	97.98	97.98	0.65	0.65	2	-
GCA_016867635.1	s__RBG-16-66-30 sp016867635	80.4359	281	519	d__Bacteria;p__Acidobacteriota;c__Aminicenantia;o__Aminicenantales;f__RBG-16-66-30;g__RBG-16-66-30	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:38:40,915] [INFO] GTDB search result was written to GCA_001773855.1_ASM177385v1_genomic.fna/result_gtdb.tsv
[2023-06-04 19:38:40,916] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:38:40,920] [INFO] DFAST_QC result json was written to GCA_001773855.1_ASM177385v1_genomic.fna/dqc_result.json
[2023-06-04 19:38:40,920] [INFO] DFAST_QC completed!
[2023-06-04 19:38:40,920] [INFO] Total running time: 0h0m47s