[2023-06-19 03:41:21,141] [INFO] DFAST_QC pipeline started.
[2023-06-19 03:41:21,145] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 03:41:21,145] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference
[2023-06-19 03:41:23,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 03:41:23,826] [INFO] Task started: Prodigal
[2023-06-19 03:41:23,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg5928e9c1-b2e1-408e-98a4-8e5bd6c25570/GCA_013696725.1_ASM1369672v1_genomic.fna.gz | prodigal -d GCA_013696725.1_ASM1369672v1_genomic.fna/cds.fna -a GCA_013696725.1_ASM1369672v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 03:41:31,533] [INFO] Task succeeded: Prodigal
[2023-06-19 03:41:31,534] [INFO] Task started: HMMsearch
[2023-06-19 03:41:31,534] [INFO] Running command: hmmsearch --tblout GCA_013696725.1_ASM1369672v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/reference_markers.hmm GCA_013696725.1_ASM1369672v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 03:41:31,724] [INFO] Task succeeded: HMMsearch
[2023-06-19 03:41:31,725] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5928e9c1-b2e1-408e-98a4-8e5bd6c25570/GCA_013696725.1_ASM1369672v1_genomic.fna.gz]
[2023-06-19 03:41:31,752] [INFO] Query marker FASTA was written to GCA_013696725.1_ASM1369672v1_genomic.fna/markers.fasta
[2023-06-19 03:41:31,753] [INFO] Task started: Blastn
[2023-06-19 03:41:31,753] [INFO] Running command: blastn -query GCA_013696725.1_ASM1369672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/reference_markers.fasta -out GCA_013696725.1_ASM1369672v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:41:32,315] [INFO] Task succeeded: Blastn
[2023-06-19 03:41:32,321] [INFO] Selected 15 target genomes.
[2023-06-19 03:41:32,321] [INFO] Target genome list was writen to GCA_013696725.1_ASM1369672v1_genomic.fna/target_genomes.txt
[2023-06-19 03:41:32,341] [INFO] Task started: fastANI
[2023-06-19 03:41:32,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg5928e9c1-b2e1-408e-98a4-8e5bd6c25570/GCA_013696725.1_ASM1369672v1_genomic.fna.gz --refList GCA_013696725.1_ASM1369672v1_genomic.fna/target_genomes.txt --output GCA_013696725.1_ASM1369672v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 03:41:42,722] [INFO] Task succeeded: fastANI
[2023-06-19 03:41:42,723] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 03:41:42,724] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 03:41:42,730] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 03:41:42,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 03:41:42,730] [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
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	76.2617	61	426	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 03:41:42,733] [INFO] DFAST Taxonomy check result was written to GCA_013696725.1_ASM1369672v1_genomic.fna/tc_result.tsv
[2023-06-19 03:41:42,733] [INFO] ===== Taxonomy check completed =====
[2023-06-19 03:41:42,733] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 03:41:42,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/checkm_data
[2023-06-19 03:41:42,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 03:41:42,770] [INFO] Task started: CheckM
[2023-06-19 03:41:42,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013696725.1_ASM1369672v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013696725.1_ASM1369672v1_genomic.fna/checkm_input GCA_013696725.1_ASM1369672v1_genomic.fna/checkm_result
[2023-06-19 03:42:10,441] [INFO] Task succeeded: CheckM
[2023-06-19 03:42:10,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.80%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 03:42:10,467] [INFO] ===== Completeness check finished =====
[2023-06-19 03:42:10,467] [INFO] ===== Start GTDB Search =====
[2023-06-19 03:42:10,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013696725.1_ASM1369672v1_genomic.fna/markers.fasta)
[2023-06-19 03:42:10,468] [INFO] Task started: Blastn
[2023-06-19 03:42:10,468] [INFO] Running command: blastn -query GCA_013696725.1_ASM1369672v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e5dfec-a420-4853-bfac-33e4faec09ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_013696725.1_ASM1369672v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 03:42:11,101] [INFO] Task succeeded: Blastn
[2023-06-19 03:42:11,106] [INFO] Selected 11 target genomes.
[2023-06-19 03:42:11,107] [INFO] Target genome list was writen to GCA_013696725.1_ASM1369672v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 03:42:11,115] [INFO] Task started: fastANI
[2023-06-19 03:42:11,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg5928e9c1-b2e1-408e-98a4-8e5bd6c25570/GCA_013696725.1_ASM1369672v1_genomic.fna.gz --refList GCA_013696725.1_ASM1369672v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013696725.1_ASM1369672v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 03:42:17,591] [INFO] Task succeeded: fastANI
[2023-06-19 03:42:17,596] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 03:42:17,596] [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_002050465.1	s__Ginsengibacter sp002050465	76.9279	55	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882215.1	s__Ginsengibacter sp017882215	76.8289	79	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710285.1	s__Ginsengibacter hankyongi	76.2617	61	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694745.1	s__Ginsengibacter sp013694745	76.2359	53	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 03:42:17,604] [INFO] GTDB search result was written to GCA_013696725.1_ASM1369672v1_genomic.fna/result_gtdb.tsv
[2023-06-19 03:42:17,604] [INFO] ===== GTDB Search completed =====
[2023-06-19 03:42:17,607] [INFO] DFAST_QC result json was written to GCA_013696725.1_ASM1369672v1_genomic.fna/dqc_result.json
[2023-06-19 03:42:17,607] [INFO] DFAST_QC completed!
[2023-06-19 03:42:17,608] [INFO] Total running time: 0h0m56s