[2023-06-19 12:10:17,944] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:10:17,946] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:10:17,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference
[2023-06-19 12:10:19,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:10:19,221] [INFO] Task started: Prodigal
[2023-06-19 12:10:19,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg35d2f3b9-ba3f-4392-b8c5-4741502c8a10/GCA_018660125.1_ASM1866012v1_genomic.fna.gz | prodigal -d GCA_018660125.1_ASM1866012v1_genomic.fna/cds.fna -a GCA_018660125.1_ASM1866012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:10:27,288] [INFO] Task succeeded: Prodigal
[2023-06-19 12:10:27,288] [INFO] Task started: HMMsearch
[2023-06-19 12:10:27,289] [INFO] Running command: hmmsearch --tblout GCA_018660125.1_ASM1866012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/reference_markers.hmm GCA_018660125.1_ASM1866012v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:10:27,529] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:10:27,530] [INFO] Found 6/6 markers.
[2023-06-19 12:10:27,563] [INFO] Query marker FASTA was written to GCA_018660125.1_ASM1866012v1_genomic.fna/markers.fasta
[2023-06-19 12:10:27,564] [INFO] Task started: Blastn
[2023-06-19 12:10:27,564] [INFO] Running command: blastn -query GCA_018660125.1_ASM1866012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/reference_markers.fasta -out GCA_018660125.1_ASM1866012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:10:28,397] [INFO] Task succeeded: Blastn
[2023-06-19 12:10:28,400] [INFO] Selected 31 target genomes.
[2023-06-19 12:10:28,401] [INFO] Target genome list was writen to GCA_018660125.1_ASM1866012v1_genomic.fna/target_genomes.txt
[2023-06-19 12:10:28,429] [INFO] Task started: fastANI
[2023-06-19 12:10:28,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d2f3b9-ba3f-4392-b8c5-4741502c8a10/GCA_018660125.1_ASM1866012v1_genomic.fna.gz --refList GCA_018660125.1_ASM1866012v1_genomic.fna/target_genomes.txt --output GCA_018660125.1_ASM1866012v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:10:43,766] [INFO] Task succeeded: fastANI
[2023-06-19 12:10:43,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:10:43,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:10:43,774] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:10:43,774] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 12:10:43,774] [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
--------------------------------------------------------------------------------
[2023-06-19 12:10:43,777] [INFO] DFAST Taxonomy check result was written to GCA_018660125.1_ASM1866012v1_genomic.fna/tc_result.tsv
[2023-06-19 12:10:43,778] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:10:43,779] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:10:43,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/checkm_data
[2023-06-19 12:10:43,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:10:43,830] [INFO] Task started: CheckM
[2023-06-19 12:10:43,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018660125.1_ASM1866012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018660125.1_ASM1866012v1_genomic.fna/checkm_input GCA_018660125.1_ASM1866012v1_genomic.fna/checkm_result
[2023-06-19 12:11:14,163] [INFO] Task succeeded: CheckM
[2023-06-19 12:11:14,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.24%
Contamintation: 10.88%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2023-06-19 12:11:14,194] [INFO] ===== Completeness check finished =====
[2023-06-19 12:11:14,195] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:11:14,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018660125.1_ASM1866012v1_genomic.fna/markers.fasta)
[2023-06-19 12:11:14,196] [INFO] Task started: Blastn
[2023-06-19 12:11:14,196] [INFO] Running command: blastn -query GCA_018660125.1_ASM1866012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3807167d-5a33-4e9f-ae13-bebeaf5c7f3b/dqc_reference/reference_markers_gtdb.fasta -out GCA_018660125.1_ASM1866012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:11:15,244] [INFO] Task succeeded: Blastn
[2023-06-19 12:11:15,247] [INFO] Selected 15 target genomes.
[2023-06-19 12:11:15,247] [INFO] Target genome list was writen to GCA_018660125.1_ASM1866012v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:11:15,255] [INFO] Task started: fastANI
[2023-06-19 12:11:15,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d2f3b9-ba3f-4392-b8c5-4741502c8a10/GCA_018660125.1_ASM1866012v1_genomic.fna.gz --refList GCA_018660125.1_ASM1866012v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018660125.1_ASM1866012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:11:23,787] [INFO] Task succeeded: fastANI
[2023-06-19 12:11:23,798] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:11:23,798] [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_018647445.1	s__UBA9926 sp018647445	99.1582	733	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	conclusive
GCA_017854255.1	s__UBA9926 sp003451575	86.9767	749	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	-
GCA_018645765.1	s__UBA9926 sp018645765	86.7667	452	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182155.1	s__UBA9926 sp905182155	80.2568	418	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689445.1	s__UBA9926 sp002689445	76.707	67	933	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:11:23,801] [INFO] GTDB search result was written to GCA_018660125.1_ASM1866012v1_genomic.fna/result_gtdb.tsv
[2023-06-19 12:11:23,802] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:11:23,805] [INFO] DFAST_QC result json was written to GCA_018660125.1_ASM1866012v1_genomic.fna/dqc_result.json
[2023-06-19 12:11:23,805] [INFO] DFAST_QC completed!
[2023-06-19 12:11:23,805] [INFO] Total running time: 0h1m6s