[2023-06-28 21:36:11,240] [INFO] DFAST_QC pipeline started.
[2023-06-28 21:36:11,242] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 21:36:11,243] [INFO] DQC Reference Directory: /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference
[2023-06-28 21:36:12,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 21:36:12,561] [INFO] Task started: Prodigal
[2023-06-28 21:36:12,561] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3e49b11-2860-4558-9a4b-9f89821c64f3/GCA_017429065.1_ASM1742906v1_genomic.fna.gz | prodigal -d GCA_017429065.1_ASM1742906v1_genomic.fna/cds.fna -a GCA_017429065.1_ASM1742906v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 21:36:21,814] [INFO] Task succeeded: Prodigal
[2023-06-28 21:36:21,815] [INFO] Task started: HMMsearch
[2023-06-28 21:36:21,815] [INFO] Running command: hmmsearch --tblout GCA_017429065.1_ASM1742906v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/reference_markers.hmm GCA_017429065.1_ASM1742906v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 21:36:22,090] [INFO] Task succeeded: HMMsearch
[2023-06-28 21:36:22,091] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3e49b11-2860-4558-9a4b-9f89821c64f3/GCA_017429065.1_ASM1742906v1_genomic.fna.gz]
[2023-06-28 21:36:22,112] [INFO] Query marker FASTA was written to GCA_017429065.1_ASM1742906v1_genomic.fna/markers.fasta
[2023-06-28 21:36:22,113] [INFO] Task started: Blastn
[2023-06-28 21:36:22,113] [INFO] Running command: blastn -query GCA_017429065.1_ASM1742906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/reference_markers.fasta -out GCA_017429065.1_ASM1742906v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:36:22,680] [INFO] Task succeeded: Blastn
[2023-06-28 21:36:22,685] [INFO] Selected 17 target genomes.
[2023-06-28 21:36:22,686] [INFO] Target genome list was writen to GCA_017429065.1_ASM1742906v1_genomic.fna/target_genomes.txt
[2023-06-28 21:36:22,690] [INFO] Task started: fastANI
[2023-06-28 21:36:22,690] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3e49b11-2860-4558-9a4b-9f89821c64f3/GCA_017429065.1_ASM1742906v1_genomic.fna.gz --refList GCA_017429065.1_ASM1742906v1_genomic.fna/target_genomes.txt --output GCA_017429065.1_ASM1742906v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 21:36:30,189] [INFO] Task succeeded: fastANI
[2023-06-28 21:36:30,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 21:36:30,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 21:36:30,191] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 21:36:30,192] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 21:36:30,192] [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
--------------------------------------------------------------------------------
[2023-06-28 21:36:30,194] [INFO] DFAST Taxonomy check result was written to GCA_017429065.1_ASM1742906v1_genomic.fna/tc_result.tsv
[2023-06-28 21:36:30,194] [INFO] ===== Taxonomy check completed =====
[2023-06-28 21:36:30,194] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 21:36:30,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/checkm_data
[2023-06-28 21:36:30,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 21:36:30,222] [INFO] Task started: CheckM
[2023-06-28 21:36:30,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017429065.1_ASM1742906v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017429065.1_ASM1742906v1_genomic.fna/checkm_input GCA_017429065.1_ASM1742906v1_genomic.fna/checkm_result
[2023-06-28 21:37:04,310] [INFO] Task succeeded: CheckM
[2023-06-28 21:37:04,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 21:37:04,332] [INFO] ===== Completeness check finished =====
[2023-06-28 21:37:04,333] [INFO] ===== Start GTDB Search =====
[2023-06-28 21:37:04,333] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017429065.1_ASM1742906v1_genomic.fna/markers.fasta)
[2023-06-28 21:37:04,333] [INFO] Task started: Blastn
[2023-06-28 21:37:04,333] [INFO] Running command: blastn -query GCA_017429065.1_ASM1742906v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1011d240-319b-4bb8-8cf0-cc90b372481d/dqc_reference/reference_markers_gtdb.fasta -out GCA_017429065.1_ASM1742906v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 21:37:05,104] [INFO] Task succeeded: Blastn
[2023-06-28 21:37:05,108] [INFO] Selected 7 target genomes.
[2023-06-28 21:37:05,108] [INFO] Target genome list was writen to GCA_017429065.1_ASM1742906v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 21:37:05,111] [INFO] Task started: fastANI
[2023-06-28 21:37:05,112] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3e49b11-2860-4558-9a4b-9f89821c64f3/GCA_017429065.1_ASM1742906v1_genomic.fna.gz --refList GCA_017429065.1_ASM1742906v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017429065.1_ASM1742906v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 21:37:08,291] [INFO] Task succeeded: fastANI
[2023-06-28 21:37:08,306] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 21:37:08,306] [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_902789435.1	s__Egerieousia sp002309115	97.3431	489	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.53	97.23	0.88	0.84	8	conclusive
GCA_902769525.1	s__Egerieousia sp902769525	88.9828	431	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	97.50	96.68	0.91	0.90	5	-
GCA_017961175.1	s__Egerieousia sp017961175	87.0444	437	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550655.1	s__Egerieousia sp017550655	84.7249	444	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	96.13	96.13	0.90	0.90	2	-
GCA_017548505.1	s__Egerieousia sp017548505	84.6455	407	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016285455.1	s__Egerieousia sp016285455	83.8567	434	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428325.1	s__Egerieousia sp017428325	83.1904	423	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Egerieousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 21:37:08,308] [INFO] GTDB search result was written to GCA_017429065.1_ASM1742906v1_genomic.fna/result_gtdb.tsv
[2023-06-28 21:37:08,309] [INFO] ===== GTDB Search completed =====
[2023-06-28 21:37:08,312] [INFO] DFAST_QC result json was written to GCA_017429065.1_ASM1742906v1_genomic.fna/dqc_result.json
[2023-06-28 21:37:08,312] [INFO] DFAST_QC completed!
[2023-06-28 21:37:08,312] [INFO] Total running time: 0h0m57s