[2023-06-13 00:23:59,896] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:23:59,898] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:23:59,898] [INFO] DQC Reference Directory: /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference
[2023-06-13 00:24:04,266] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:24:04,268] [INFO] Task started: Prodigal
[2023-06-13 00:24:04,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eb6f0ac-93d8-4ec2-9f8f-ef19d3e08e72/GCA_022708405.1_ASM2270840v1_genomic.fna.gz | prodigal -d GCA_022708405.1_ASM2270840v1_genomic.fna/cds.fna -a GCA_022708405.1_ASM2270840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:24:21,836] [INFO] Task succeeded: Prodigal
[2023-06-13 00:24:21,837] [INFO] Task started: HMMsearch
[2023-06-13 00:24:21,837] [INFO] Running command: hmmsearch --tblout GCA_022708405.1_ASM2270840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/reference_markers.hmm GCA_022708405.1_ASM2270840v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:24:22,106] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:24:22,109] [INFO] Found 6/6 markers.
[2023-06-13 00:24:22,183] [INFO] Query marker FASTA was written to GCA_022708405.1_ASM2270840v1_genomic.fna/markers.fasta
[2023-06-13 00:24:22,183] [INFO] Task started: Blastn
[2023-06-13 00:24:22,184] [INFO] Running command: blastn -query GCA_022708405.1_ASM2270840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/reference_markers.fasta -out GCA_022708405.1_ASM2270840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:24:22,772] [INFO] Task succeeded: Blastn
[2023-06-13 00:24:22,780] [INFO] Selected 33 target genomes.
[2023-06-13 00:24:22,781] [INFO] Target genome list was writen to GCA_022708405.1_ASM2270840v1_genomic.fna/target_genomes.txt
[2023-06-13 00:24:22,792] [INFO] Task started: fastANI
[2023-06-13 00:24:22,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb6f0ac-93d8-4ec2-9f8f-ef19d3e08e72/GCA_022708405.1_ASM2270840v1_genomic.fna.gz --refList GCA_022708405.1_ASM2270840v1_genomic.fna/target_genomes.txt --output GCA_022708405.1_ASM2270840v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:24:43,255] [INFO] Task succeeded: fastANI
[2023-06-13 00:24:43,256] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:24:43,256] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:24:43,258] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 00:24:43,259] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 00:24:43,259] [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
--------------------------------------------------------------------------------
[2023-06-13 00:24:43,261] [INFO] DFAST Taxonomy check result was written to GCA_022708405.1_ASM2270840v1_genomic.fna/tc_result.tsv
[2023-06-13 00:24:43,262] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:24:43,262] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:24:43,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/checkm_data
[2023-06-13 00:24:43,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:24:43,316] [INFO] Task started: CheckM
[2023-06-13 00:24:43,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708405.1_ASM2270840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708405.1_ASM2270840v1_genomic.fna/checkm_input GCA_022708405.1_ASM2270840v1_genomic.fna/checkm_result
[2023-06-13 00:25:36,423] [INFO] Task succeeded: CheckM
[2023-06-13 00:25:36,425] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 2.60%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-13 00:25:36,452] [INFO] ===== Completeness check finished =====
[2023-06-13 00:25:36,452] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:25:36,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708405.1_ASM2270840v1_genomic.fna/markers.fasta)
[2023-06-13 00:25:36,453] [INFO] Task started: Blastn
[2023-06-13 00:25:36,453] [INFO] Running command: blastn -query GCA_022708405.1_ASM2270840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83b5fad3-bca3-492e-95f7-f4bd7633407c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708405.1_ASM2270840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:25:37,252] [INFO] Task succeeded: Blastn
[2023-06-13 00:25:37,259] [INFO] Selected 28 target genomes.
[2023-06-13 00:25:37,259] [INFO] Target genome list was writen to GCA_022708405.1_ASM2270840v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:25:37,276] [INFO] Task started: fastANI
[2023-06-13 00:25:37,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eb6f0ac-93d8-4ec2-9f8f-ef19d3e08e72/GCA_022708405.1_ASM2270840v1_genomic.fna.gz --refList GCA_022708405.1_ASM2270840v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708405.1_ASM2270840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:25:54,399] [INFO] Task succeeded: fastANI
[2023-06-13 00:25:54,411] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:25:54,411] [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_012719495.1	s__SKHV01 sp012719495	97.3829	1003	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016938055.1	s__SKHV01 sp016938055	76.686	61	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998095.1	s__SKHV01 sp017998095	76.4991	55	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016930365.1	s__SKHV01 sp016930365	76.2731	59	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	99.95	99.95	0.83	0.83	2	-
GCA_007116765.1	s__SKHV01 sp007116765	76.188	63	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933815.1	s__SKHV01 sp016933815	76.1383	74	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931385.1	s__SKHV01 sp016931385	75.7452	66	1171	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__SKHV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 00:25:54,415] [INFO] GTDB search result was written to GCA_022708405.1_ASM2270840v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:25:54,416] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:25:54,419] [INFO] DFAST_QC result json was written to GCA_022708405.1_ASM2270840v1_genomic.fna/dqc_result.json
[2023-06-13 00:25:54,419] [INFO] DFAST_QC completed!
[2023-06-13 00:25:54,420] [INFO] Total running time: 0h1m55s