[2023-06-19 02:46:01,373] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:46:01,375] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:46:01,375] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference
[2023-06-19 02:46:02,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:46:02,597] [INFO] Task started: Prodigal
[2023-06-19 02:46:02,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d79f075-2e5a-49d6-b052-9e366b45faf2/GCA_018607705.1_ASM1860770v1_genomic.fna.gz | prodigal -d GCA_018607705.1_ASM1860770v1_genomic.fna/cds.fna -a GCA_018607705.1_ASM1860770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:46:10,532] [INFO] Task succeeded: Prodigal
[2023-06-19 02:46:10,532] [INFO] Task started: HMMsearch
[2023-06-19 02:46:10,532] [INFO] Running command: hmmsearch --tblout GCA_018607705.1_ASM1860770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/reference_markers.hmm GCA_018607705.1_ASM1860770v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:46:10,865] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:46:10,866] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d79f075-2e5a-49d6-b052-9e366b45faf2/GCA_018607705.1_ASM1860770v1_genomic.fna.gz]
[2023-06-19 02:46:10,898] [INFO] Query marker FASTA was written to GCA_018607705.1_ASM1860770v1_genomic.fna/markers.fasta
[2023-06-19 02:46:10,898] [INFO] Task started: Blastn
[2023-06-19 02:46:10,898] [INFO] Running command: blastn -query GCA_018607705.1_ASM1860770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/reference_markers.fasta -out GCA_018607705.1_ASM1860770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:11,567] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:11,570] [INFO] Selected 29 target genomes.
[2023-06-19 02:46:11,571] [INFO] Target genome list was writen to GCA_018607705.1_ASM1860770v1_genomic.fna/target_genomes.txt
[2023-06-19 02:46:11,573] [INFO] Task started: fastANI
[2023-06-19 02:46:11,573] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d79f075-2e5a-49d6-b052-9e366b45faf2/GCA_018607705.1_ASM1860770v1_genomic.fna.gz --refList GCA_018607705.1_ASM1860770v1_genomic.fna/target_genomes.txt --output GCA_018607705.1_ASM1860770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:46:31,732] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:31,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:46:31,733] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:46:31,734] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:46:31,735] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:46:31,735] [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 02:46:31,737] [INFO] DFAST Taxonomy check result was written to GCA_018607705.1_ASM1860770v1_genomic.fna/tc_result.tsv
[2023-06-19 02:46:31,737] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:46:31,737] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:46:31,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/checkm_data
[2023-06-19 02:46:31,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:46:31,782] [INFO] Task started: CheckM
[2023-06-19 02:46:31,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607705.1_ASM1860770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607705.1_ASM1860770v1_genomic.fna/checkm_input GCA_018607705.1_ASM1860770v1_genomic.fna/checkm_result
[2023-06-19 02:47:01,778] [INFO] Task succeeded: CheckM
[2023-06-19 02:47:01,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:47:01,797] [INFO] ===== Completeness check finished =====
[2023-06-19 02:47:01,798] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:47:01,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607705.1_ASM1860770v1_genomic.fna/markers.fasta)
[2023-06-19 02:47:01,798] [INFO] Task started: Blastn
[2023-06-19 02:47:01,799] [INFO] Running command: blastn -query GCA_018607705.1_ASM1860770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e2d6523-d8e0-4fa4-9a58-24bb663b06d9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607705.1_ASM1860770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:47:02,803] [INFO] Task succeeded: Blastn
[2023-06-19 02:47:02,808] [INFO] Selected 19 target genomes.
[2023-06-19 02:47:02,808] [INFO] Target genome list was writen to GCA_018607705.1_ASM1860770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:47:02,818] [INFO] Task started: fastANI
[2023-06-19 02:47:02,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d79f075-2e5a-49d6-b052-9e366b45faf2/GCA_018607705.1_ASM1860770v1_genomic.fna.gz --refList GCA_018607705.1_ASM1860770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607705.1_ASM1860770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:47:16,231] [INFO] Task succeeded: fastANI
[2023-06-19 02:47:16,239] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:47:16,239] [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_002389265.1	s__UBA4582 sp002389265	99.3198	781	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	99.27	99.04	0.79	0.76	8	conclusive
GCA_018607725.1	s__UBA4582 sp002386885	92.6958	794	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	99.32	99.32	0.90	0.90	2	-
GCA_013204195.1	s__UBA4582 sp013204195	88.2463	543	946	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4582	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:47:16,242] [INFO] GTDB search result was written to GCA_018607705.1_ASM1860770v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:47:16,242] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:47:16,245] [INFO] DFAST_QC result json was written to GCA_018607705.1_ASM1860770v1_genomic.fna/dqc_result.json
[2023-06-19 02:47:16,246] [INFO] DFAST_QC completed!
[2023-06-19 02:47:16,246] [INFO] Total running time: 0h1m15s