[2023-06-18 11:16:09,979] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:16:09,981] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:16:09,981] [INFO] DQC Reference Directory: /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference
[2023-06-18 11:16:11,200] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:16:11,201] [INFO] Task started: Prodigal
[2023-06-18 11:16:11,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg342f6390-e6f4-46cf-9843-be9ea34c68f2/GCA_018697355.1_ASM1869735v1_genomic.fna.gz | prodigal -d GCA_018697355.1_ASM1869735v1_genomic.fna/cds.fna -a GCA_018697355.1_ASM1869735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:16:24,472] [INFO] Task succeeded: Prodigal
[2023-06-18 11:16:24,472] [INFO] Task started: HMMsearch
[2023-06-18 11:16:24,472] [INFO] Running command: hmmsearch --tblout GCA_018697355.1_ASM1869735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/reference_markers.hmm GCA_018697355.1_ASM1869735v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:16:24,784] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:16:24,785] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg342f6390-e6f4-46cf-9843-be9ea34c68f2/GCA_018697355.1_ASM1869735v1_genomic.fna.gz]
[2023-06-18 11:16:24,844] [INFO] Query marker FASTA was written to GCA_018697355.1_ASM1869735v1_genomic.fna/markers.fasta
[2023-06-18 11:16:24,845] [INFO] Task started: Blastn
[2023-06-18 11:16:24,845] [INFO] Running command: blastn -query GCA_018697355.1_ASM1869735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/reference_markers.fasta -out GCA_018697355.1_ASM1869735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:16:25,407] [INFO] Task succeeded: Blastn
[2023-06-18 11:16:25,411] [INFO] Selected 16 target genomes.
[2023-06-18 11:16:25,412] [INFO] Target genome list was writen to GCA_018697355.1_ASM1869735v1_genomic.fna/target_genomes.txt
[2023-06-18 11:16:25,415] [INFO] Task started: fastANI
[2023-06-18 11:16:25,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg342f6390-e6f4-46cf-9843-be9ea34c68f2/GCA_018697355.1_ASM1869735v1_genomic.fna.gz --refList GCA_018697355.1_ASM1869735v1_genomic.fna/target_genomes.txt --output GCA_018697355.1_ASM1869735v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:16:33,666] [INFO] Task succeeded: fastANI
[2023-06-18 11:16:33,667] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:16:33,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:16:33,669] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 11:16:33,669] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 11:16:33,669] [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
--------------------------------------------------------------------------------
[2023-06-18 11:16:33,671] [INFO] DFAST Taxonomy check result was written to GCA_018697355.1_ASM1869735v1_genomic.fna/tc_result.tsv
[2023-06-18 11:16:33,671] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:16:33,672] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:16:33,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/checkm_data
[2023-06-18 11:16:33,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:16:33,742] [INFO] Task started: CheckM
[2023-06-18 11:16:33,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018697355.1_ASM1869735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018697355.1_ASM1869735v1_genomic.fna/checkm_input GCA_018697355.1_ASM1869735v1_genomic.fna/checkm_result
[2023-06-18 11:17:18,187] [INFO] Task succeeded: CheckM
[2023-06-18 11:17:18,189] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:17:18,212] [INFO] ===== Completeness check finished =====
[2023-06-18 11:17:18,213] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:17:18,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018697355.1_ASM1869735v1_genomic.fna/markers.fasta)
[2023-06-18 11:17:18,213] [INFO] Task started: Blastn
[2023-06-18 11:17:18,214] [INFO] Running command: blastn -query GCA_018697355.1_ASM1869735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdfbf2f33-0f7e-4f8f-a319-5e04cfedbef2/dqc_reference/reference_markers_gtdb.fasta -out GCA_018697355.1_ASM1869735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:17:18,926] [INFO] Task succeeded: Blastn
[2023-06-18 11:17:18,930] [INFO] Selected 21 target genomes.
[2023-06-18 11:17:18,930] [INFO] Target genome list was writen to GCA_018697355.1_ASM1869735v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:17:19,013] [INFO] Task started: fastANI
[2023-06-18 11:17:19,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg342f6390-e6f4-46cf-9843-be9ea34c68f2/GCA_018697355.1_ASM1869735v1_genomic.fna.gz --refList GCA_018697355.1_ASM1869735v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018697355.1_ASM1869735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:17:31,652] [INFO] Task succeeded: fastANI
[2023-06-18 11:17:31,658] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:17:31,659] [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_018645005.1	s__JAHJRI01 sp018645005	98.7692	755	1608	d__Bacteria;p__SAR324;c__SAR324;o__XYD2-FULL-50-16;f__XYD2-FULL-50-16;g__JAHJRI01	95.0	99.66	99.41	0.88	0.82	6	conclusive
GCA_018830885.1	s__JAHJRI01 sp018830885	77.0625	353	1608	d__Bacteria;p__SAR324;c__SAR324;o__XYD2-FULL-50-16;f__XYD2-FULL-50-16;g__JAHJRI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:17:31,661] [INFO] GTDB search result was written to GCA_018697355.1_ASM1869735v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:17:31,661] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:17:31,663] [INFO] DFAST_QC result json was written to GCA_018697355.1_ASM1869735v1_genomic.fna/dqc_result.json
[2023-06-18 11:17:31,663] [INFO] DFAST_QC completed!
[2023-06-18 11:17:31,663] [INFO] Total running time: 0h1m22s