[2023-06-08 17:28:03,226] [INFO] DFAST_QC pipeline started.
[2023-06-08 17:28:03,230] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 17:28:03,231] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference
[2023-06-08 17:28:04,677] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 17:28:04,678] [INFO] Task started: Prodigal
[2023-06-08 17:28:04,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg7071d848-b0ef-4ab3-866a-5c4429c4106b/GCA_947466565.1_RH-14apr17-128_genomic.fna.gz | prodigal -d GCA_947466565.1_RH-14apr17-128_genomic.fna/cds.fna -a GCA_947466565.1_RH-14apr17-128_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 17:28:11,960] [INFO] Task succeeded: Prodigal
[2023-06-08 17:28:11,960] [INFO] Task started: HMMsearch
[2023-06-08 17:28:11,960] [INFO] Running command: hmmsearch --tblout GCA_947466565.1_RH-14apr17-128_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/reference_markers.hmm GCA_947466565.1_RH-14apr17-128_genomic.fna/protein.faa > /dev/null
[2023-06-08 17:28:12,212] [INFO] Task succeeded: HMMsearch
[2023-06-08 17:28:12,214] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7071d848-b0ef-4ab3-866a-5c4429c4106b/GCA_947466565.1_RH-14apr17-128_genomic.fna.gz]
[2023-06-08 17:28:12,241] [INFO] Query marker FASTA was written to GCA_947466565.1_RH-14apr17-128_genomic.fna/markers.fasta
[2023-06-08 17:28:12,242] [INFO] Task started: Blastn
[2023-06-08 17:28:12,242] [INFO] Running command: blastn -query GCA_947466565.1_RH-14apr17-128_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/reference_markers.fasta -out GCA_947466565.1_RH-14apr17-128_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:28:12,839] [INFO] Task succeeded: Blastn
[2023-06-08 17:28:12,843] [INFO] Selected 28 target genomes.
[2023-06-08 17:28:12,844] [INFO] Target genome list was writen to GCA_947466565.1_RH-14apr17-128_genomic.fna/target_genomes.txt
[2023-06-08 17:28:12,850] [INFO] Task started: fastANI
[2023-06-08 17:28:12,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg7071d848-b0ef-4ab3-866a-5c4429c4106b/GCA_947466565.1_RH-14apr17-128_genomic.fna.gz --refList GCA_947466565.1_RH-14apr17-128_genomic.fna/target_genomes.txt --output GCA_947466565.1_RH-14apr17-128_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 17:28:28,239] [INFO] Task succeeded: fastANI
[2023-06-08 17:28:28,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 17:28:28,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 17:28:28,241] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 17:28:28,241] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 17:28:28,242] [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
--------------------------------------------------------------------------------
[2023-06-08 17:28:28,244] [INFO] DFAST Taxonomy check result was written to GCA_947466565.1_RH-14apr17-128_genomic.fna/tc_result.tsv
[2023-06-08 17:28:28,244] [INFO] ===== Taxonomy check completed =====
[2023-06-08 17:28:28,244] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 17:28:28,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/checkm_data
[2023-06-08 17:28:28,247] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 17:28:28,275] [INFO] Task started: CheckM
[2023-06-08 17:28:28,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947466565.1_RH-14apr17-128_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947466565.1_RH-14apr17-128_genomic.fna/checkm_input GCA_947466565.1_RH-14apr17-128_genomic.fna/checkm_result
[2023-06-08 17:28:55,005] [INFO] Task succeeded: CheckM
[2023-06-08 17:28:55,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 17:28:55,033] [INFO] ===== Completeness check finished =====
[2023-06-08 17:28:55,033] [INFO] ===== Start GTDB Search =====
[2023-06-08 17:28:55,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947466565.1_RH-14apr17-128_genomic.fna/markers.fasta)
[2023-06-08 17:28:55,034] [INFO] Task started: Blastn
[2023-06-08 17:28:55,034] [INFO] Running command: blastn -query GCA_947466565.1_RH-14apr17-128_genomic.fna/markers.fasta -db /var/lib/cwl/stgd12f540b-4336-4a92-bed7-75ea0ecee7e5/dqc_reference/reference_markers_gtdb.fasta -out GCA_947466565.1_RH-14apr17-128_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 17:28:55,816] [INFO] Task succeeded: Blastn
[2023-06-08 17:28:55,820] [INFO] Selected 8 target genomes.
[2023-06-08 17:28:55,820] [INFO] Target genome list was writen to GCA_947466565.1_RH-14apr17-128_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 17:28:55,822] [INFO] Task started: fastANI
[2023-06-08 17:28:55,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg7071d848-b0ef-4ab3-866a-5c4429c4106b/GCA_947466565.1_RH-14apr17-128_genomic.fna.gz --refList GCA_947466565.1_RH-14apr17-128_genomic.fna/target_genomes_gtdb.txt --output GCA_947466565.1_RH-14apr17-128_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 17:28:59,174] [INFO] Task succeeded: fastANI
[2023-06-08 17:28:59,187] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 17:28:59,187] [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_903824725.1	s__Sediminibacterium sp903824725	99.0697	553	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903953815.1	s__Sediminibacterium sp903953815	80.8845	363	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.40	99.39	0.85	0.84	4	-
GCA_005800655.1	s__Sediminibacterium sp005800655	80.7411	358	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693715.1	s__Sediminibacterium sp009693715	80.7174	336	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910765.1	s__Sediminibacterium sp903910765	80.6734	329	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003509845.1	s__Sediminibacterium sp003509845	79.9885	275	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938445.1	s__Sediminibacterium sp903938445	78.456	259	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.86	99.85	0.95	0.95	3	-
GCA_903929425.1	s__Sediminibacterium sp903929425	78.128	222	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 17:28:59,189] [INFO] GTDB search result was written to GCA_947466565.1_RH-14apr17-128_genomic.fna/result_gtdb.tsv
[2023-06-08 17:28:59,190] [INFO] ===== GTDB Search completed =====
[2023-06-08 17:28:59,194] [INFO] DFAST_QC result json was written to GCA_947466565.1_RH-14apr17-128_genomic.fna/dqc_result.json
[2023-06-08 17:28:59,194] [INFO] DFAST_QC completed!
[2023-06-08 17:28:59,195] [INFO] Total running time: 0h0m56s