[2023-06-19 05:25:11,219] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:25:11,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:25:11,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference
[2023-06-19 05:25:12,551] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:25:12,552] [INFO] Task started: Prodigal
[2023-06-19 05:25:12,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg408546d9-f2c8-400e-92c8-99219d708887/GCA_018900255.1_ASM1890025v1_genomic.fna.gz | prodigal -d GCA_018900255.1_ASM1890025v1_genomic.fna/cds.fna -a GCA_018900255.1_ASM1890025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:25:18,730] [INFO] Task succeeded: Prodigal
[2023-06-19 05:25:18,731] [INFO] Task started: HMMsearch
[2023-06-19 05:25:18,731] [INFO] Running command: hmmsearch --tblout GCA_018900255.1_ASM1890025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/reference_markers.hmm GCA_018900255.1_ASM1890025v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:25:19,011] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:25:19,012] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg408546d9-f2c8-400e-92c8-99219d708887/GCA_018900255.1_ASM1890025v1_genomic.fna.gz]
[2023-06-19 05:25:19,077] [INFO] Query marker FASTA was written to GCA_018900255.1_ASM1890025v1_genomic.fna/markers.fasta
[2023-06-19 05:25:19,078] [INFO] Task started: Blastn
[2023-06-19 05:25:19,078] [INFO] Running command: blastn -query GCA_018900255.1_ASM1890025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/reference_markers.fasta -out GCA_018900255.1_ASM1890025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:19,656] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:19,664] [INFO] Selected 11 target genomes.
[2023-06-19 05:25:19,664] [INFO] Target genome list was writen to GCA_018900255.1_ASM1890025v1_genomic.fna/target_genomes.txt
[2023-06-19 05:25:19,668] [INFO] Task started: fastANI
[2023-06-19 05:25:19,669] [INFO] Running command: fastANI --query /var/lib/cwl/stg408546d9-f2c8-400e-92c8-99219d708887/GCA_018900255.1_ASM1890025v1_genomic.fna.gz --refList GCA_018900255.1_ASM1890025v1_genomic.fna/target_genomes.txt --output GCA_018900255.1_ASM1890025v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:25,910] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:25,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:25,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:25,913] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:25:25,913] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 05:25:25,913] [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 05:25:25,916] [INFO] DFAST Taxonomy check result was written to GCA_018900255.1_ASM1890025v1_genomic.fna/tc_result.tsv
[2023-06-19 05:25:25,916] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:25,917] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:25,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/checkm_data
[2023-06-19 05:25:25,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:25,958] [INFO] Task started: CheckM
[2023-06-19 05:25:25,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018900255.1_ASM1890025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018900255.1_ASM1890025v1_genomic.fna/checkm_input GCA_018900255.1_ASM1890025v1_genomic.fna/checkm_result
[2023-06-19 05:25:51,410] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:51,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.25%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:51,445] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:51,446] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:51,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018900255.1_ASM1890025v1_genomic.fna/markers.fasta)
[2023-06-19 05:25:51,447] [INFO] Task started: Blastn
[2023-06-19 05:25:51,447] [INFO] Running command: blastn -query GCA_018900255.1_ASM1890025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7acf7ad-38e0-4799-a98f-b41f1195d11d/dqc_reference/reference_markers_gtdb.fasta -out GCA_018900255.1_ASM1890025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:52,207] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:52,234] [INFO] Selected 12 target genomes.
[2023-06-19 05:25:52,235] [INFO] Target genome list was writen to GCA_018900255.1_ASM1890025v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:52,277] [INFO] Task started: fastANI
[2023-06-19 05:25:52,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg408546d9-f2c8-400e-92c8-99219d708887/GCA_018900255.1_ASM1890025v1_genomic.fna.gz --refList GCA_018900255.1_ASM1890025v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018900255.1_ASM1890025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:58,170] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:58,179] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:25:58,180] [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_018901125.1	s__RPRI01 sp018901125	99.5704	568	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018817425.1	s__RPRI01 sp018817425	82.6719	434	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011391695.1	s__RPRI01 sp011391695	77.3353	64	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830925.1	s__RPRI01 sp018830925	77.2628	61	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819005.1	s__RPRI01 sp018819005	77.1602	51	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823005.1	s__RPRI01 sp018823005	76.6194	52	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818505.1	s__RPRI01 sp003818505	76.5097	75	632	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__RPRI01;g__RPRI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:58,182] [INFO] GTDB search result was written to GCA_018900255.1_ASM1890025v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:58,182] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:58,185] [INFO] DFAST_QC result json was written to GCA_018900255.1_ASM1890025v1_genomic.fna/dqc_result.json
[2023-06-19 05:25:58,185] [INFO] DFAST_QC completed!
[2023-06-19 05:25:58,185] [INFO] Total running time: 0h0m47s