[2023-06-28 16:21:30,696] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:21:30,698] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:21:30,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference
[2023-06-28 16:21:31,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:21:31,890] [INFO] Task started: Prodigal
[2023-06-28 16:21:31,890] [INFO] Running command: gunzip -c /var/lib/cwl/stg7d4b554f-57e2-4499-8913-8434fae1fb9f/GCA_012103405.1_ASM1210340v1_genomic.fna.gz | prodigal -d GCA_012103405.1_ASM1210340v1_genomic.fna/cds.fna -a GCA_012103405.1_ASM1210340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:21:45,196] [INFO] Task succeeded: Prodigal
[2023-06-28 16:21:45,197] [INFO] Task started: HMMsearch
[2023-06-28 16:21:45,197] [INFO] Running command: hmmsearch --tblout GCA_012103405.1_ASM1210340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/reference_markers.hmm GCA_012103405.1_ASM1210340v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:21:45,417] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:21:45,419] [INFO] Found 6/6 markers.
[2023-06-28 16:21:45,459] [INFO] Query marker FASTA was written to GCA_012103405.1_ASM1210340v1_genomic.fna/markers.fasta
[2023-06-28 16:21:45,459] [INFO] Task started: Blastn
[2023-06-28 16:21:45,460] [INFO] Running command: blastn -query GCA_012103405.1_ASM1210340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/reference_markers.fasta -out GCA_012103405.1_ASM1210340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:21:46,155] [INFO] Task succeeded: Blastn
[2023-06-28 16:21:46,159] [INFO] Selected 28 target genomes.
[2023-06-28 16:21:46,159] [INFO] Target genome list was writen to GCA_012103405.1_ASM1210340v1_genomic.fna/target_genomes.txt
[2023-06-28 16:21:46,160] [INFO] Task started: fastANI
[2023-06-28 16:21:46,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d4b554f-57e2-4499-8913-8434fae1fb9f/GCA_012103405.1_ASM1210340v1_genomic.fna.gz --refList GCA_012103405.1_ASM1210340v1_genomic.fna/target_genomes.txt --output GCA_012103405.1_ASM1210340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:22:08,840] [INFO] Task succeeded: fastANI
[2023-06-28 16:22:08,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:22:08,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:22:08,843] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:22:08,843] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:22:08,843] [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
--------------------------------------------------------------------------------
[2023-06-28 16:22:08,845] [INFO] DFAST Taxonomy check result was written to GCA_012103405.1_ASM1210340v1_genomic.fna/tc_result.tsv
[2023-06-28 16:22:08,845] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:22:08,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:22:08,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/checkm_data
[2023-06-28 16:22:08,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:22:08,889] [INFO] Task started: CheckM
[2023-06-28 16:22:08,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012103405.1_ASM1210340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012103405.1_ASM1210340v1_genomic.fna/checkm_input GCA_012103405.1_ASM1210340v1_genomic.fna/checkm_result
[2023-06-28 16:22:50,780] [INFO] Task succeeded: CheckM
[2023-06-28 16:22:50,781] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:22:50,802] [INFO] ===== Completeness check finished =====
[2023-06-28 16:22:50,802] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:22:50,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012103405.1_ASM1210340v1_genomic.fna/markers.fasta)
[2023-06-28 16:22:50,803] [INFO] Task started: Blastn
[2023-06-28 16:22:50,803] [INFO] Running command: blastn -query GCA_012103405.1_ASM1210340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b93f7ef-a6e7-4349-a552-7c98d4a32855/dqc_reference/reference_markers_gtdb.fasta -out GCA_012103405.1_ASM1210340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:22:51,907] [INFO] Task succeeded: Blastn
[2023-06-28 16:22:51,913] [INFO] Selected 18 target genomes.
[2023-06-28 16:22:51,913] [INFO] Target genome list was writen to GCA_012103405.1_ASM1210340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:22:51,926] [INFO] Task started: fastANI
[2023-06-28 16:22:51,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg7d4b554f-57e2-4499-8913-8434fae1fb9f/GCA_012103405.1_ASM1210340v1_genomic.fna.gz --refList GCA_012103405.1_ASM1210340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012103405.1_ASM1210340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:23:07,291] [INFO] Task succeeded: fastANI
[2023-06-28 16:23:07,298] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:23:07,298] [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_011087605.1	s__R2A130 sp011087605	99.9579	1224	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	99.98	99.97	0.98	0.98	3	conclusive
GCA_014238155.1	s__R2A130 sp014238155	83.0902	1077	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214695.1	s__R2A130 sp013214695	77.9752	346	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480295.1	s__R2A130 sp905480295	77.7201	268	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179775.1	s__R2A130 sp000179775	76.9726	97	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__R2A130	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009744025.1	s__Allorhizobium vitis_A	75.7346	52	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.14	95.73	0.87	0.84	24	-
GCF_001758275.2	s__Allorhizobium vitis_B	75.3656	57	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.87	95.34	0.94	0.85	14	-
--------------------------------------------------------------------------------
[2023-06-28 16:23:07,300] [INFO] GTDB search result was written to GCA_012103405.1_ASM1210340v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:23:07,301] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:23:07,304] [INFO] DFAST_QC result json was written to GCA_012103405.1_ASM1210340v1_genomic.fna/dqc_result.json
[2023-06-28 16:23:07,304] [INFO] DFAST_QC completed!
[2023-06-28 16:23:07,304] [INFO] Total running time: 0h1m37s