[2023-06-14 01:07:23,129] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:23,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:23,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference
[2023-06-14 01:07:24,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:24,462] [INFO] Task started: Prodigal
[2023-06-14 01:07:24,463] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6e69d90-2f62-4a2a-9266-f18b331c48e0/GCA_022360375.1_ASM2236037v1_genomic.fna.gz | prodigal -d GCA_022360375.1_ASM2236037v1_genomic.fna/cds.fna -a GCA_022360375.1_ASM2236037v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:36,406] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:36,407] [INFO] Task started: HMMsearch
[2023-06-14 01:07:36,407] [INFO] Running command: hmmsearch --tblout GCA_022360375.1_ASM2236037v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/reference_markers.hmm GCA_022360375.1_ASM2236037v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:36,647] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:36,648] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb6e69d90-2f62-4a2a-9266-f18b331c48e0/GCA_022360375.1_ASM2236037v1_genomic.fna.gz]
[2023-06-14 01:07:36,676] [INFO] Query marker FASTA was written to GCA_022360375.1_ASM2236037v1_genomic.fna/markers.fasta
[2023-06-14 01:07:36,676] [INFO] Task started: Blastn
[2023-06-14 01:07:36,676] [INFO] Running command: blastn -query GCA_022360375.1_ASM2236037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/reference_markers.fasta -out GCA_022360375.1_ASM2236037v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:37,246] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:37,250] [INFO] Selected 15 target genomes.
[2023-06-14 01:07:37,250] [INFO] Target genome list was writen to GCA_022360375.1_ASM2236037v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:37,255] [INFO] Task started: fastANI
[2023-06-14 01:07:37,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e69d90-2f62-4a2a-9266-f18b331c48e0/GCA_022360375.1_ASM2236037v1_genomic.fna.gz --refList GCA_022360375.1_ASM2236037v1_genomic.fna/target_genomes.txt --output GCA_022360375.1_ASM2236037v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:07:47,558] [INFO] Task succeeded: fastANI
[2023-06-14 01:07:47,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:07:47,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:07:47,561] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:07:47,562] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:07:47,562] [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
--------------------------------------------------------------------------------
[2023-06-14 01:07:47,564] [INFO] DFAST Taxonomy check result was written to GCA_022360375.1_ASM2236037v1_genomic.fna/tc_result.tsv
[2023-06-14 01:07:47,565] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:07:47,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:07:47,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/checkm_data
[2023-06-14 01:07:47,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:07:47,602] [INFO] Task started: CheckM
[2023-06-14 01:07:47,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022360375.1_ASM2236037v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022360375.1_ASM2236037v1_genomic.fna/checkm_input GCA_022360375.1_ASM2236037v1_genomic.fna/checkm_result
[2023-06-14 01:08:26,875] [INFO] Task succeeded: CheckM
[2023-06-14 01:08:26,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 3.62%
Strain heterogeneity: 11.11%
--------------------------------------------------------------------------------
[2023-06-14 01:08:26,900] [INFO] ===== Completeness check finished =====
[2023-06-14 01:08:26,900] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:08:26,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022360375.1_ASM2236037v1_genomic.fna/markers.fasta)
[2023-06-14 01:08:26,901] [INFO] Task started: Blastn
[2023-06-14 01:08:26,901] [INFO] Running command: blastn -query GCA_022360375.1_ASM2236037v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg96ef0035-60d3-4e18-8403-ddbebac5813f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022360375.1_ASM2236037v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:08:27,695] [INFO] Task succeeded: Blastn
[2023-06-14 01:08:27,699] [INFO] Selected 21 target genomes.
[2023-06-14 01:08:27,700] [INFO] Target genome list was writen to GCA_022360375.1_ASM2236037v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:08:27,716] [INFO] Task started: fastANI
[2023-06-14 01:08:27,716] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6e69d90-2f62-4a2a-9266-f18b331c48e0/GCA_022360375.1_ASM2236037v1_genomic.fna.gz --refList GCA_022360375.1_ASM2236037v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022360375.1_ASM2236037v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:08:37,732] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:37,743] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:08:37,743] [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_017643365.1	s__HXMU1420-13 sp017643365	77.2834	58	725	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712055.1	s__RHLJ01 sp003712055	76.8984	78	725	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640605.1	s__HXMU1420-13 sp017640605	76.7054	63	725	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__HXMU1420-13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640665.1	s__RHLJ01 sp017640665	76.4261	80	725	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	100.00	100.00	1.00	1.00	3	-
GCA_017795005.1	s__RHLJ01 sp017795005	76.3281	82	725	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__RHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:08:37,745] [INFO] GTDB search result was written to GCA_022360375.1_ASM2236037v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:08:37,746] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:08:37,749] [INFO] DFAST_QC result json was written to GCA_022360375.1_ASM2236037v1_genomic.fna/dqc_result.json
[2023-06-14 01:08:37,750] [INFO] DFAST_QC completed!
[2023-06-14 01:08:37,750] [INFO] Total running time: 0h1m15s