[2023-06-18 13:03:41,815] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:03:41,852] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:03:41,852] [INFO] DQC Reference Directory: /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference
[2023-06-18 13:03:43,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:03:43,081] [INFO] Task started: Prodigal
[2023-06-18 13:03:43,082] [INFO] Running command: gunzip -c /var/lib/cwl/stga98bf1a5-7b9f-4fc8-8063-e50de4897cac/GCA_018006875.1_ASM1800687v1_genomic.fna.gz | prodigal -d GCA_018006875.1_ASM1800687v1_genomic.fna/cds.fna -a GCA_018006875.1_ASM1800687v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:03:48,387] [INFO] Task succeeded: Prodigal
[2023-06-18 13:03:48,388] [INFO] Task started: HMMsearch
[2023-06-18 13:03:48,388] [INFO] Running command: hmmsearch --tblout GCA_018006875.1_ASM1800687v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/reference_markers.hmm GCA_018006875.1_ASM1800687v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:03:48,564] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:03:48,565] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga98bf1a5-7b9f-4fc8-8063-e50de4897cac/GCA_018006875.1_ASM1800687v1_genomic.fna.gz]
[2023-06-18 13:03:48,588] [INFO] Query marker FASTA was written to GCA_018006875.1_ASM1800687v1_genomic.fna/markers.fasta
[2023-06-18 13:03:48,589] [INFO] Task started: Blastn
[2023-06-18 13:03:48,589] [INFO] Running command: blastn -query GCA_018006875.1_ASM1800687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/reference_markers.fasta -out GCA_018006875.1_ASM1800687v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:03:49,271] [INFO] Task succeeded: Blastn
[2023-06-18 13:03:49,277] [INFO] Selected 16 target genomes.
[2023-06-18 13:03:49,278] [INFO] Target genome list was writen to GCA_018006875.1_ASM1800687v1_genomic.fna/target_genomes.txt
[2023-06-18 13:03:49,282] [INFO] Task started: fastANI
[2023-06-18 13:03:49,282] [INFO] Running command: fastANI --query /var/lib/cwl/stga98bf1a5-7b9f-4fc8-8063-e50de4897cac/GCA_018006875.1_ASM1800687v1_genomic.fna.gz --refList GCA_018006875.1_ASM1800687v1_genomic.fna/target_genomes.txt --output GCA_018006875.1_ASM1800687v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:04:00,210] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:00,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:04:00,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:04:00,213] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:04:00,213] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:04:00,213] [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 13:04:00,215] [INFO] DFAST Taxonomy check result was written to GCA_018006875.1_ASM1800687v1_genomic.fna/tc_result.tsv
[2023-06-18 13:04:00,216] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:04:00,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:04:00,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/checkm_data
[2023-06-18 13:04:00,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:04:00,250] [INFO] Task started: CheckM
[2023-06-18 13:04:00,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018006875.1_ASM1800687v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018006875.1_ASM1800687v1_genomic.fna/checkm_input GCA_018006875.1_ASM1800687v1_genomic.fna/checkm_result
[2023-06-18 13:04:21,349] [INFO] Task succeeded: CheckM
[2023-06-18 13:04:21,352] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:04:21,378] [INFO] ===== Completeness check finished =====
[2023-06-18 13:04:21,378] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:04:21,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018006875.1_ASM1800687v1_genomic.fna/markers.fasta)
[2023-06-18 13:04:21,378] [INFO] Task started: Blastn
[2023-06-18 13:04:21,379] [INFO] Running command: blastn -query GCA_018006875.1_ASM1800687v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41852a5e-8b76-4e5f-ae6d-ba86748dc1c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018006875.1_ASM1800687v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:04:22,428] [INFO] Task succeeded: Blastn
[2023-06-18 13:04:22,432] [INFO] Selected 19 target genomes.
[2023-06-18 13:04:22,432] [INFO] Target genome list was writen to GCA_018006875.1_ASM1800687v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:04:22,506] [INFO] Task started: fastANI
[2023-06-18 13:04:22,506] [INFO] Running command: fastANI --query /var/lib/cwl/stga98bf1a5-7b9f-4fc8-8063-e50de4897cac/GCA_018006875.1_ASM1800687v1_genomic.fna.gz --refList GCA_018006875.1_ASM1800687v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018006875.1_ASM1800687v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:04:33,463] [INFO] Task succeeded: fastANI
[2023-06-18 13:04:33,467] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:04:33,467] [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_017998555.1	s__JADKDT01 sp017998555	98.2283	366	487	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__J036;g__JADKDT01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016714465.1	s__JADKDT01 sp016714465	86.4846	397	487	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Thermoflexales;f__J036;g__JADKDT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:04:33,471] [INFO] GTDB search result was written to GCA_018006875.1_ASM1800687v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:04:33,472] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:04:33,476] [INFO] DFAST_QC result json was written to GCA_018006875.1_ASM1800687v1_genomic.fna/dqc_result.json
[2023-06-18 13:04:33,476] [INFO] DFAST_QC completed!
[2023-06-18 13:04:33,476] [INFO] Total running time: 0h0m52s