[2023-06-19 00:05:15,230] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:05:15,236] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:05:15,237] [INFO] DQC Reference Directory: /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference
[2023-06-19 00:05:16,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:05:16,542] [INFO] Task started: Prodigal
[2023-06-19 00:05:16,543] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0f12b65-6789-4874-8055-68bf73fab457/GCA_018695175.1_ASM1869517v1_genomic.fna.gz | prodigal -d GCA_018695175.1_ASM1869517v1_genomic.fna/cds.fna -a GCA_018695175.1_ASM1869517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:05:23,267] [INFO] Task succeeded: Prodigal
[2023-06-19 00:05:23,267] [INFO] Task started: HMMsearch
[2023-06-19 00:05:23,267] [INFO] Running command: hmmsearch --tblout GCA_018695175.1_ASM1869517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/reference_markers.hmm GCA_018695175.1_ASM1869517v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:05:23,530] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:05:23,532] [INFO] Found 6/6 markers.
[2023-06-19 00:05:23,584] [INFO] Query marker FASTA was written to GCA_018695175.1_ASM1869517v1_genomic.fna/markers.fasta
[2023-06-19 00:05:23,585] [INFO] Task started: Blastn
[2023-06-19 00:05:23,585] [INFO] Running command: blastn -query GCA_018695175.1_ASM1869517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/reference_markers.fasta -out GCA_018695175.1_ASM1869517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:05:24,206] [INFO] Task succeeded: Blastn
[2023-06-19 00:05:24,223] [INFO] Selected 42 target genomes.
[2023-06-19 00:05:24,224] [INFO] Target genome list was writen to GCA_018695175.1_ASM1869517v1_genomic.fna/target_genomes.txt
[2023-06-19 00:05:24,240] [INFO] Task started: fastANI
[2023-06-19 00:05:24,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0f12b65-6789-4874-8055-68bf73fab457/GCA_018695175.1_ASM1869517v1_genomic.fna.gz --refList GCA_018695175.1_ASM1869517v1_genomic.fna/target_genomes.txt --output GCA_018695175.1_ASM1869517v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:05:50,160] [INFO] Task succeeded: fastANI
[2023-06-19 00:05:50,161] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:05:50,161] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:05:50,163] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:05:50,163] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 00:05:50,163] [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 00:05:50,165] [INFO] DFAST Taxonomy check result was written to GCA_018695175.1_ASM1869517v1_genomic.fna/tc_result.tsv
[2023-06-19 00:05:50,166] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:05:50,166] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:05:50,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/checkm_data
[2023-06-19 00:05:50,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:05:50,261] [INFO] Task started: CheckM
[2023-06-19 00:05:50,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018695175.1_ASM1869517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018695175.1_ASM1869517v1_genomic.fna/checkm_input GCA_018695175.1_ASM1869517v1_genomic.fna/checkm_result
[2023-06-19 00:06:17,673] [INFO] Task succeeded: CheckM
[2023-06-19 00:06:17,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.23%
Contamintation: 5.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-19 00:06:17,740] [INFO] ===== Completeness check finished =====
[2023-06-19 00:06:17,740] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:06:17,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018695175.1_ASM1869517v1_genomic.fna/markers.fasta)
[2023-06-19 00:06:17,741] [INFO] Task started: Blastn
[2023-06-19 00:06:17,741] [INFO] Running command: blastn -query GCA_018695175.1_ASM1869517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeede9c66-ffcc-412f-b215-4bfa86b94da2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018695175.1_ASM1869517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:06:18,581] [INFO] Task succeeded: Blastn
[2023-06-19 00:06:18,586] [INFO] Selected 35 target genomes.
[2023-06-19 00:06:18,587] [INFO] Target genome list was writen to GCA_018695175.1_ASM1869517v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:06:18,602] [INFO] Task started: fastANI
[2023-06-19 00:06:18,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0f12b65-6789-4874-8055-68bf73fab457/GCA_018695175.1_ASM1869517v1_genomic.fna.gz --refList GCA_018695175.1_ASM1869517v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018695175.1_ASM1869517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:06:36,849] [INFO] Task succeeded: fastANI
[2023-06-19 00:06:36,854] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:06:36,854] [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_013349825.1	s__Thiopontia sp013349825	99.61	655	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.78	99.58	0.88	0.82	21	conclusive
GCA_018648825.1	s__Thiopontia sp018648825	82.4697	243	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.74	99.68	0.85	0.80	15	-
GCA_014384675.1	s__Thiopontia autotrophica	77.9354	106	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	99.91	99.91	0.96	0.96	2	-
GCA_018671205.1	s__Thiopontia sp018671205	77.3192	148	801	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCF-002020875;f__GCF-002020875;g__Thiopontia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:06:36,860] [INFO] GTDB search result was written to GCA_018695175.1_ASM1869517v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:06:36,861] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:06:36,873] [INFO] DFAST_QC result json was written to GCA_018695175.1_ASM1869517v1_genomic.fna/dqc_result.json
[2023-06-19 00:06:36,873] [INFO] DFAST_QC completed!
[2023-06-19 00:06:36,873] [INFO] Total running time: 0h1m22s