[2023-06-19 08:45:48,073] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:48,075] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:48,075] [INFO] DQC Reference Directory: /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference
[2023-06-19 08:45:49,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:49,360] [INFO] Task started: Prodigal
[2023-06-19 08:45:49,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg20ad40d8-3d77-4af8-a430-2d58a35405c6/GCA_018399455.1_ASM1839945v1_genomic.fna.gz | prodigal -d GCA_018399455.1_ASM1839945v1_genomic.fna/cds.fna -a GCA_018399455.1_ASM1839945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:55,602] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:55,602] [INFO] Task started: HMMsearch
[2023-06-19 08:45:55,602] [INFO] Running command: hmmsearch --tblout GCA_018399455.1_ASM1839945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/reference_markers.hmm GCA_018399455.1_ASM1839945v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:55,892] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:55,896] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg20ad40d8-3d77-4af8-a430-2d58a35405c6/GCA_018399455.1_ASM1839945v1_genomic.fna.gz]
[2023-06-19 08:45:55,939] [INFO] Query marker FASTA was written to GCA_018399455.1_ASM1839945v1_genomic.fna/markers.fasta
[2023-06-19 08:45:55,940] [INFO] Task started: Blastn
[2023-06-19 08:45:55,940] [INFO] Running command: blastn -query GCA_018399455.1_ASM1839945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/reference_markers.fasta -out GCA_018399455.1_ASM1839945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:56,511] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:56,515] [INFO] Selected 20 target genomes.
[2023-06-19 08:45:56,515] [INFO] Target genome list was writen to GCA_018399455.1_ASM1839945v1_genomic.fna/target_genomes.txt
[2023-06-19 08:45:56,521] [INFO] Task started: fastANI
[2023-06-19 08:45:56,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ad40d8-3d77-4af8-a430-2d58a35405c6/GCA_018399455.1_ASM1839945v1_genomic.fna.gz --refList GCA_018399455.1_ASM1839945v1_genomic.fna/target_genomes.txt --output GCA_018399455.1_ASM1839945v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:46:08,060] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:08,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:46:08,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:46:08,062] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:46:08,062] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:46:08,062] [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 08:46:08,064] [INFO] DFAST Taxonomy check result was written to GCA_018399455.1_ASM1839945v1_genomic.fna/tc_result.tsv
[2023-06-19 08:46:08,065] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:46:08,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:46:08,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/checkm_data
[2023-06-19 08:46:08,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:46:08,102] [INFO] Task started: CheckM
[2023-06-19 08:46:08,102] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018399455.1_ASM1839945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018399455.1_ASM1839945v1_genomic.fna/checkm_input GCA_018399455.1_ASM1839945v1_genomic.fna/checkm_result
[2023-06-19 08:46:32,962] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:32,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.91%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:32,997] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:32,998] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:32,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018399455.1_ASM1839945v1_genomic.fna/markers.fasta)
[2023-06-19 08:46:32,999] [INFO] Task started: Blastn
[2023-06-19 08:46:32,999] [INFO] Running command: blastn -query GCA_018399455.1_ASM1839945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb50e5c44-be42-4399-82eb-d638c7ceddbe/dqc_reference/reference_markers_gtdb.fasta -out GCA_018399455.1_ASM1839945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:33,814] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:33,818] [INFO] Selected 18 target genomes.
[2023-06-19 08:46:33,819] [INFO] Target genome list was writen to GCA_018399455.1_ASM1839945v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:33,845] [INFO] Task started: fastANI
[2023-06-19 08:46:33,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg20ad40d8-3d77-4af8-a430-2d58a35405c6/GCA_018399455.1_ASM1839945v1_genomic.fna.gz --refList GCA_018399455.1_ASM1839945v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018399455.1_ASM1839945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:43,867] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:43,876] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:46:43,876] [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_018399455.1	s__M55B175 sp018399455	100.0	586	594	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__M55B175	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018334555.1	s__M55B175 sp018334555	77.0932	107	594	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__M55B175	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399235.1	s__M55B175 sp018399235	76.9042	80	594	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__SURF-3;g__M55B175	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:43,881] [INFO] GTDB search result was written to GCA_018399455.1_ASM1839945v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:43,882] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:43,885] [INFO] DFAST_QC result json was written to GCA_018399455.1_ASM1839945v1_genomic.fna/dqc_result.json
[2023-06-19 08:46:43,885] [INFO] DFAST_QC completed!
[2023-06-19 08:46:43,885] [INFO] Total running time: 0h0m56s