[2023-06-19 14:29:46,559] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:29:46,561] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:29:46,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference
[2023-06-19 14:29:48,199] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:29:48,200] [INFO] Task started: Prodigal
[2023-06-19 14:29:48,200] [INFO] Running command: gunzip -c /var/lib/cwl/stg2268de3e-4872-4f4a-a0c8-8af4a183fc97/GCA_018652515.1_ASM1865251v1_genomic.fna.gz | prodigal -d GCA_018652515.1_ASM1865251v1_genomic.fna/cds.fna -a GCA_018652515.1_ASM1865251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:29:51,496] [INFO] Task succeeded: Prodigal
[2023-06-19 14:29:51,496] [INFO] Task started: HMMsearch
[2023-06-19 14:29:51,496] [INFO] Running command: hmmsearch --tblout GCA_018652515.1_ASM1865251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/reference_markers.hmm GCA_018652515.1_ASM1865251v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:29:51,776] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:29:51,779] [INFO] Found 6/6 markers.
[2023-06-19 14:29:51,800] [INFO] Query marker FASTA was written to GCA_018652515.1_ASM1865251v1_genomic.fna/markers.fasta
[2023-06-19 14:29:51,800] [INFO] Task started: Blastn
[2023-06-19 14:29:51,801] [INFO] Running command: blastn -query GCA_018652515.1_ASM1865251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/reference_markers.fasta -out GCA_018652515.1_ASM1865251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:29:52,482] [INFO] Task succeeded: Blastn
[2023-06-19 14:29:52,488] [INFO] Selected 37 target genomes.
[2023-06-19 14:29:52,489] [INFO] Target genome list was writen to GCA_018652515.1_ASM1865251v1_genomic.fna/target_genomes.txt
[2023-06-19 14:29:52,525] [INFO] Task started: fastANI
[2023-06-19 14:29:52,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg2268de3e-4872-4f4a-a0c8-8af4a183fc97/GCA_018652515.1_ASM1865251v1_genomic.fna.gz --refList GCA_018652515.1_ASM1865251v1_genomic.fna/target_genomes.txt --output GCA_018652515.1_ASM1865251v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:30:19,736] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:19,737] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:30:19,737] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:30:19,739] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:30:19,739] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 14:30:19,739] [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
--------------------------------------------------------------------------------
[2023-06-19 14:30:19,741] [INFO] DFAST Taxonomy check result was written to GCA_018652515.1_ASM1865251v1_genomic.fna/tc_result.tsv
[2023-06-19 14:30:19,741] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:30:19,742] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:30:19,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/checkm_data
[2023-06-19 14:30:19,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:30:19,763] [INFO] Task started: CheckM
[2023-06-19 14:30:19,763] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018652515.1_ASM1865251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018652515.1_ASM1865251v1_genomic.fna/checkm_input GCA_018652515.1_ASM1865251v1_genomic.fna/checkm_result
[2023-06-19 14:30:38,016] [INFO] Task succeeded: CheckM
[2023-06-19 14:30:38,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:30:38,044] [INFO] ===== Completeness check finished =====
[2023-06-19 14:30:38,044] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:30:38,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018652515.1_ASM1865251v1_genomic.fna/markers.fasta)
[2023-06-19 14:30:38,045] [INFO] Task started: Blastn
[2023-06-19 14:30:38,045] [INFO] Running command: blastn -query GCA_018652515.1_ASM1865251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e3d83d6-7b5e-487d-aca9-3f6cab48c73c/dqc_reference/reference_markers_gtdb.fasta -out GCA_018652515.1_ASM1865251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:30:38,932] [INFO] Task succeeded: Blastn
[2023-06-19 14:30:38,938] [INFO] Selected 17 target genomes.
[2023-06-19 14:30:38,938] [INFO] Target genome list was writen to GCA_018652515.1_ASM1865251v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:30:38,946] [INFO] Task started: fastANI
[2023-06-19 14:30:38,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg2268de3e-4872-4f4a-a0c8-8af4a183fc97/GCA_018652515.1_ASM1865251v1_genomic.fna.gz --refList GCA_018652515.1_ASM1865251v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018652515.1_ASM1865251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:30:42,661] [INFO] Task succeeded: fastANI
[2023-06-19 14:30:42,673] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:30:42,673] [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_004214015.1	s__MED-G11 sp004214015	97.9159	230	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.90	97.77	0.83	0.80	4	conclusive
GCA_016777325.1	s__MED-G11 sp016777325	91.876	214	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509805.1	s__MED-G11 sp902509805	90.7613	165	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	97.79	97.79	0.58	0.58	2	-
GCA_018646865.1	s__MED-G11 sp014239615	86.3048	293	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.76	99.49	0.92	0.80	17	-
GCA_902514615.1	s__MED-G11 sp902514615	85.1565	232	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239665.1	s__MED-G11 sp014239665	83.3611	274	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.49	96.27	0.81	0.77	10	-
GCA_002457075.1	s__MED-G11 sp002457075	82.8205	219	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	98.35	98.35	0.79	0.79	2	-
GCA_902622595.1	s__MED-G11 sp902622595	78.9667	219	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	96.81	96.16	0.93	0.91	12	-
GCA_016780245.1	s__MED-G11 sp016780245	78.5795	155	374	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G11	95.0	99.94	99.94	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-19 14:30:42,676] [INFO] GTDB search result was written to GCA_018652515.1_ASM1865251v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:30:42,676] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:30:42,679] [INFO] DFAST_QC result json was written to GCA_018652515.1_ASM1865251v1_genomic.fna/dqc_result.json
[2023-06-19 14:30:42,680] [INFO] DFAST_QC completed!
[2023-06-19 14:30:42,680] [INFO] Total running time: 0h0m56s