[2023-06-18 18:33:42,406] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:33:42,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:33:42,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference
[2023-06-18 18:33:43,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:33:43,616] [INFO] Task started: Prodigal
[2023-06-18 18:33:43,617] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0243370-f3a9-4970-8c49-d500503d3465/GCA_018673435.1_ASM1867343v1_genomic.fna.gz | prodigal -d GCA_018673435.1_ASM1867343v1_genomic.fna/cds.fna -a GCA_018673435.1_ASM1867343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:33:49,299] [INFO] Task succeeded: Prodigal
[2023-06-18 18:33:49,300] [INFO] Task started: HMMsearch
[2023-06-18 18:33:49,300] [INFO] Running command: hmmsearch --tblout GCA_018673435.1_ASM1867343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/reference_markers.hmm GCA_018673435.1_ASM1867343v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:33:49,539] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:33:49,541] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf0243370-f3a9-4970-8c49-d500503d3465/GCA_018673435.1_ASM1867343v1_genomic.fna.gz]
[2023-06-18 18:33:49,572] [INFO] Query marker FASTA was written to GCA_018673435.1_ASM1867343v1_genomic.fna/markers.fasta
[2023-06-18 18:33:49,573] [INFO] Task started: Blastn
[2023-06-18 18:33:49,573] [INFO] Running command: blastn -query GCA_018673435.1_ASM1867343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/reference_markers.fasta -out GCA_018673435.1_ASM1867343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:33:50,146] [INFO] Task succeeded: Blastn
[2023-06-18 18:33:50,151] [INFO] Selected 15 target genomes.
[2023-06-18 18:33:50,151] [INFO] Target genome list was writen to GCA_018673435.1_ASM1867343v1_genomic.fna/target_genomes.txt
[2023-06-18 18:33:50,156] [INFO] Task started: fastANI
[2023-06-18 18:33:50,157] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0243370-f3a9-4970-8c49-d500503d3465/GCA_018673435.1_ASM1867343v1_genomic.fna.gz --refList GCA_018673435.1_ASM1867343v1_genomic.fna/target_genomes.txt --output GCA_018673435.1_ASM1867343v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:33:56,594] [INFO] Task succeeded: fastANI
[2023-06-18 18:33:56,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:33:56,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:33:56,597] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:33:56,598] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:33:56,598] [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 18:33:56,607] [INFO] DFAST Taxonomy check result was written to GCA_018673435.1_ASM1867343v1_genomic.fna/tc_result.tsv
[2023-06-18 18:33:56,609] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:33:56,610] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:33:56,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/checkm_data
[2023-06-18 18:33:56,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:33:56,654] [INFO] Task started: CheckM
[2023-06-18 18:33:56,654] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018673435.1_ASM1867343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018673435.1_ASM1867343v1_genomic.fna/checkm_input GCA_018673435.1_ASM1867343v1_genomic.fna/checkm_result
[2023-06-18 18:34:19,886] [INFO] Task succeeded: CheckM
[2023-06-18 18:34:19,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.57%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:34:19,908] [INFO] ===== Completeness check finished =====
[2023-06-18 18:34:19,909] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:34:19,909] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018673435.1_ASM1867343v1_genomic.fna/markers.fasta)
[2023-06-18 18:34:19,910] [INFO] Task started: Blastn
[2023-06-18 18:34:19,910] [INFO] Running command: blastn -query GCA_018673435.1_ASM1867343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg510734e0-df1c-4ad8-b726-f68d943ef0c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018673435.1_ASM1867343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:34:20,692] [INFO] Task succeeded: Blastn
[2023-06-18 18:34:20,698] [INFO] Selected 22 target genomes.
[2023-06-18 18:34:20,698] [INFO] Target genome list was writen to GCA_018673435.1_ASM1867343v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:34:20,710] [INFO] Task started: fastANI
[2023-06-18 18:34:20,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0243370-f3a9-4970-8c49-d500503d3465/GCA_018673435.1_ASM1867343v1_genomic.fna.gz --refList GCA_018673435.1_ASM1867343v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018673435.1_ASM1867343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:34:27,188] [INFO] Task succeeded: fastANI
[2023-06-18 18:34:27,195] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:34:27,196] [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_002708305.1	s__UBA7326 sp002708305	98.029	670	863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	98.40	98.02	0.79	0.75	5	conclusive
GCA_003284265.1	s__UBA7326 sp003284265	77.7895	131	863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002709155.1	s__UBA7326 sp002709155	77.2913	112	863	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__UBA7326	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:34:27,198] [INFO] GTDB search result was written to GCA_018673435.1_ASM1867343v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:34:27,199] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:34:27,201] [INFO] DFAST_QC result json was written to GCA_018673435.1_ASM1867343v1_genomic.fna/dqc_result.json
[2023-06-18 18:34:27,201] [INFO] DFAST_QC completed!
[2023-06-18 18:34:27,201] [INFO] Total running time: 0h0m45s