[2023-06-13 17:33:31,949] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:33:31,951] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:33:31,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference
[2023-06-13 17:33:33,308] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:33:33,309] [INFO] Task started: Prodigal
[2023-06-13 17:33:33,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg96b7313b-481f-4679-b949-fa90f0ffd22e/GCA_947482585.1_RH-27jun17-358_genomic.fna.gz | prodigal -d GCA_947482585.1_RH-27jun17-358_genomic.fna/cds.fna -a GCA_947482585.1_RH-27jun17-358_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:33:39,899] [INFO] Task succeeded: Prodigal
[2023-06-13 17:33:39,899] [INFO] Task started: HMMsearch
[2023-06-13 17:33:39,899] [INFO] Running command: hmmsearch --tblout GCA_947482585.1_RH-27jun17-358_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/reference_markers.hmm GCA_947482585.1_RH-27jun17-358_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:33:40,083] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:33:40,085] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg96b7313b-481f-4679-b949-fa90f0ffd22e/GCA_947482585.1_RH-27jun17-358_genomic.fna.gz]
[2023-06-13 17:33:40,110] [INFO] Query marker FASTA was written to GCA_947482585.1_RH-27jun17-358_genomic.fna/markers.fasta
[2023-06-13 17:33:40,110] [INFO] Task started: Blastn
[2023-06-13 17:33:40,110] [INFO] Running command: blastn -query GCA_947482585.1_RH-27jun17-358_genomic.fna/markers.fasta -db /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/reference_markers.fasta -out GCA_947482585.1_RH-27jun17-358_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:33:40,694] [INFO] Task succeeded: Blastn
[2023-06-13 17:33:40,697] [INFO] Selected 19 target genomes.
[2023-06-13 17:33:40,697] [INFO] Target genome list was writen to GCA_947482585.1_RH-27jun17-358_genomic.fna/target_genomes.txt
[2023-06-13 17:33:40,701] [INFO] Task started: fastANI
[2023-06-13 17:33:40,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7313b-481f-4679-b949-fa90f0ffd22e/GCA_947482585.1_RH-27jun17-358_genomic.fna.gz --refList GCA_947482585.1_RH-27jun17-358_genomic.fna/target_genomes.txt --output GCA_947482585.1_RH-27jun17-358_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:33:49,919] [INFO] Task succeeded: fastANI
[2023-06-13 17:33:49,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:33:49,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:33:49,921] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:33:49,921] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 17:33:49,921] [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
--------------------------------------------------------------------------------
[2023-06-13 17:33:49,926] [INFO] DFAST Taxonomy check result was written to GCA_947482585.1_RH-27jun17-358_genomic.fna/tc_result.tsv
[2023-06-13 17:33:49,927] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:33:49,928] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:33:49,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/checkm_data
[2023-06-13 17:33:49,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:33:49,957] [INFO] Task started: CheckM
[2023-06-13 17:33:49,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947482585.1_RH-27jun17-358_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947482585.1_RH-27jun17-358_genomic.fna/checkm_input GCA_947482585.1_RH-27jun17-358_genomic.fna/checkm_result
[2023-06-13 17:34:14,195] [INFO] Task succeeded: CheckM
[2023-06-13 17:34:14,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.13%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:34:14,216] [INFO] ===== Completeness check finished =====
[2023-06-13 17:34:14,216] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:34:14,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947482585.1_RH-27jun17-358_genomic.fna/markers.fasta)
[2023-06-13 17:34:14,217] [INFO] Task started: Blastn
[2023-06-13 17:34:14,217] [INFO] Running command: blastn -query GCA_947482585.1_RH-27jun17-358_genomic.fna/markers.fasta -db /var/lib/cwl/stg27934eb0-8f82-44cf-ba00-efc11b334a5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947482585.1_RH-27jun17-358_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:34:15,015] [INFO] Task succeeded: Blastn
[2023-06-13 17:34:15,020] [INFO] Selected 10 target genomes.
[2023-06-13 17:34:15,020] [INFO] Target genome list was writen to GCA_947482585.1_RH-27jun17-358_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:34:15,021] [INFO] Task started: fastANI
[2023-06-13 17:34:15,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg96b7313b-481f-4679-b949-fa90f0ffd22e/GCA_947482585.1_RH-27jun17-358_genomic.fna.gz --refList GCA_947482585.1_RH-27jun17-358_genomic.fna/target_genomes_gtdb.txt --output GCA_947482585.1_RH-27jun17-358_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:34:21,603] [INFO] Task succeeded: fastANI
[2023-06-13 17:34:21,609] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:34:21,609] [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_903866355.1	s__Ga0077536 sp903866355	95.9712	488	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009692365.1	s__Ga0077536 sp009692365	84.1918	504	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464935.1	s__Ga0077536 sp001464935	75.9172	86	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719885.1	s__JADJYF01 sp016719885	75.7024	59	686	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 17:34:21,611] [INFO] GTDB search result was written to GCA_947482585.1_RH-27jun17-358_genomic.fna/result_gtdb.tsv
[2023-06-13 17:34:21,612] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:34:21,614] [INFO] DFAST_QC result json was written to GCA_947482585.1_RH-27jun17-358_genomic.fna/dqc_result.json
[2023-06-13 17:34:21,614] [INFO] DFAST_QC completed!
[2023-06-13 17:34:21,615] [INFO] Total running time: 0h0m50s