[2023-06-19 10:56:17,367] [INFO] DFAST_QC pipeline started.
[2023-06-19 10:56:17,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 10:56:17,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference
[2023-06-19 10:56:18,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 10:56:18,596] [INFO] Task started: Prodigal
[2023-06-19 10:56:18,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg063476bd-61ed-425b-8c2a-459bdd742f68/GCA_018607685.1_ASM1860768v1_genomic.fna.gz | prodigal -d GCA_018607685.1_ASM1860768v1_genomic.fna/cds.fna -a GCA_018607685.1_ASM1860768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 10:56:26,338] [INFO] Task succeeded: Prodigal
[2023-06-19 10:56:26,339] [INFO] Task started: HMMsearch
[2023-06-19 10:56:26,339] [INFO] Running command: hmmsearch --tblout GCA_018607685.1_ASM1860768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/reference_markers.hmm GCA_018607685.1_ASM1860768v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 10:56:26,597] [INFO] Task succeeded: HMMsearch
[2023-06-19 10:56:26,598] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg063476bd-61ed-425b-8c2a-459bdd742f68/GCA_018607685.1_ASM1860768v1_genomic.fna.gz]
[2023-06-19 10:56:26,633] [INFO] Query marker FASTA was written to GCA_018607685.1_ASM1860768v1_genomic.fna/markers.fasta
[2023-06-19 10:56:26,634] [INFO] Task started: Blastn
[2023-06-19 10:56:26,634] [INFO] Running command: blastn -query GCA_018607685.1_ASM1860768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/reference_markers.fasta -out GCA_018607685.1_ASM1860768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:56:27,273] [INFO] Task succeeded: Blastn
[2023-06-19 10:56:27,278] [INFO] Selected 28 target genomes.
[2023-06-19 10:56:27,279] [INFO] Target genome list was writen to GCA_018607685.1_ASM1860768v1_genomic.fna/target_genomes.txt
[2023-06-19 10:56:27,285] [INFO] Task started: fastANI
[2023-06-19 10:56:27,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg063476bd-61ed-425b-8c2a-459bdd742f68/GCA_018607685.1_ASM1860768v1_genomic.fna.gz --refList GCA_018607685.1_ASM1860768v1_genomic.fna/target_genomes.txt --output GCA_018607685.1_ASM1860768v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 10:56:44,443] [INFO] Task succeeded: fastANI
[2023-06-19 10:56:44,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 10:56:44,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 10:56:44,445] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 10:56:44,446] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 10:56:44,446] [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 10:56:44,447] [INFO] DFAST Taxonomy check result was written to GCA_018607685.1_ASM1860768v1_genomic.fna/tc_result.tsv
[2023-06-19 10:56:44,448] [INFO] ===== Taxonomy check completed =====
[2023-06-19 10:56:44,448] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 10:56:44,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/checkm_data
[2023-06-19 10:56:44,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 10:56:44,495] [INFO] Task started: CheckM
[2023-06-19 10:56:44,495] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607685.1_ASM1860768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607685.1_ASM1860768v1_genomic.fna/checkm_input GCA_018607685.1_ASM1860768v1_genomic.fna/checkm_result
[2023-06-19 10:57:14,337] [INFO] Task succeeded: CheckM
[2023-06-19 10:57:14,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.48%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 10:57:14,367] [INFO] ===== Completeness check finished =====
[2023-06-19 10:57:14,368] [INFO] ===== Start GTDB Search =====
[2023-06-19 10:57:14,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607685.1_ASM1860768v1_genomic.fna/markers.fasta)
[2023-06-19 10:57:14,369] [INFO] Task started: Blastn
[2023-06-19 10:57:14,369] [INFO] Running command: blastn -query GCA_018607685.1_ASM1860768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc15c2e6-b8c6-4421-a047-511651233bcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607685.1_ASM1860768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 10:57:15,373] [INFO] Task succeeded: Blastn
[2023-06-19 10:57:15,378] [INFO] Selected 13 target genomes.
[2023-06-19 10:57:15,378] [INFO] Target genome list was writen to GCA_018607685.1_ASM1860768v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 10:57:15,385] [INFO] Task started: fastANI
[2023-06-19 10:57:15,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg063476bd-61ed-425b-8c2a-459bdd742f68/GCA_018607685.1_ASM1860768v1_genomic.fna.gz --refList GCA_018607685.1_ASM1860768v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607685.1_ASM1860768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 10:57:23,456] [INFO] Task succeeded: fastANI
[2023-06-19 10:57:23,468] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 10:57:23,468] [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_018607685.1	s__UBA9659 sp018607685	100.0	916	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012961165.1	s__UBA9659 sp012961165	82.5462	597	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018665025.1	s__UBA9659 sp018665025	81.5656	548	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_018645845.1	s__UBA9659 sp018645845	79.9777	398	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
GCA_018667205.1	s__UBA9659 sp018667205	78.95	322	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779585.1	s__UBA9659 sp016779585	75.9856	79	932	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 10:57:23,470] [INFO] GTDB search result was written to GCA_018607685.1_ASM1860768v1_genomic.fna/result_gtdb.tsv
[2023-06-19 10:57:23,471] [INFO] ===== GTDB Search completed =====
[2023-06-19 10:57:23,473] [INFO] DFAST_QC result json was written to GCA_018607685.1_ASM1860768v1_genomic.fna/dqc_result.json
[2023-06-19 10:57:23,473] [INFO] DFAST_QC completed!
[2023-06-19 10:57:23,474] [INFO] Total running time: 0h1m6s