[2024-01-24 13:25:27,783] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:27,785] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:27,785] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference
[2024-01-24 13:25:29,034] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:29,034] [INFO] Task started: Prodigal
[2024-01-24 13:25:29,035] [INFO] Running command: gunzip -c /var/lib/cwl/stg59b6139a-d2aa-43c4-919b-8b6f18ef22db/GCF_002897375.1_ASM289737v1_genomic.fna.gz | prodigal -d GCF_002897375.1_ASM289737v1_genomic.fna/cds.fna -a GCF_002897375.1_ASM289737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:54,864] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:54,865] [INFO] Task started: HMMsearch
[2024-01-24 13:25:54,865] [INFO] Running command: hmmsearch --tblout GCF_002897375.1_ASM289737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/reference_markers.hmm GCF_002897375.1_ASM289737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:55,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:55,129] [INFO] Found 6/6 markers.
[2024-01-24 13:25:55,168] [INFO] Query marker FASTA was written to GCF_002897375.1_ASM289737v1_genomic.fna/markers.fasta
[2024-01-24 13:25:55,169] [INFO] Task started: Blastn
[2024-01-24 13:25:55,169] [INFO] Running command: blastn -query GCF_002897375.1_ASM289737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/reference_markers.fasta -out GCF_002897375.1_ASM289737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:55,923] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:55,926] [INFO] Selected 9 target genomes.
[2024-01-24 13:25:55,926] [INFO] Target genome list was writen to GCF_002897375.1_ASM289737v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:55,931] [INFO] Task started: fastANI
[2024-01-24 13:25:55,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b6139a-d2aa-43c4-919b-8b6f18ef22db/GCF_002897375.1_ASM289737v1_genomic.fna.gz --refList GCF_002897375.1_ASM289737v1_genomic.fna/target_genomes.txt --output GCF_002897375.1_ASM289737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:05,486] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:05,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:05,488] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:05,500] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:05,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:05,500] [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
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	100.0	1484	1486	95	conclusive
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	90.0752	1046	1486	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	85.5294	955	1486	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	85.4215	998	1486	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	85.4073	993	1486	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	84.8296	918	1486	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	83.0874	827	1486	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	82.2307	760	1486	95	below_threshold
Deinococcus radiopugnans	strain=DSM 12027	GCA_014201625.1	57497	57497	type	True	79.2059	625	1486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:05,502] [INFO] DFAST Taxonomy check result was written to GCF_002897375.1_ASM289737v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:05,503] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:05,503] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:05,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/checkm_data
[2024-01-24 13:26:05,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:05,560] [INFO] Task started: CheckM
[2024-01-24 13:26:05,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002897375.1_ASM289737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002897375.1_ASM289737v1_genomic.fna/checkm_input GCF_002897375.1_ASM289737v1_genomic.fna/checkm_result
[2024-01-24 13:26:57,882] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:57,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:57,907] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:57,907] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:57,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002897375.1_ASM289737v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:57,908] [INFO] Task started: Blastn
[2024-01-24 13:26:57,908] [INFO] Running command: blastn -query GCF_002897375.1_ASM289737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c562a3d-909b-4c72-8fd1-d0f8b0c17b1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002897375.1_ASM289737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:58,895] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:58,899] [INFO] Selected 8 target genomes.
[2024-01-24 13:26:58,899] [INFO] Target genome list was writen to GCF_002897375.1_ASM289737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:58,915] [INFO] Task started: fastANI
[2024-01-24 13:26:58,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b6139a-d2aa-43c4-919b-8b6f18ef22db/GCF_002897375.1_ASM289737v1_genomic.fna.gz --refList GCF_002897375.1_ASM289737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002897375.1_ASM289737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:07,477] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:07,489] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:07,489] [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
GCF_002897375.1	s__Deinococcus aerius	100.0	1484	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000381345.1	s__Deinococcus apachensis	90.0752	1046	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004758605.1	s__Deinococcus metallilatus	85.4444	996	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_002869765.1	s__Deinococcus planocerae	84.8058	920	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863415.1	s__Deinococcus sp018863415	83.9782	959	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000599865.1	s__Deinococcus phoenicis	83.0833	828	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201885.1	s__Deinococcus budaensis	82.8188	862	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377345.1	s__Deinococcus sp009377345	82.2169	762	1486	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:07,491] [INFO] GTDB search result was written to GCF_002897375.1_ASM289737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:07,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:07,494] [INFO] DFAST_QC result json was written to GCF_002897375.1_ASM289737v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:07,494] [INFO] DFAST_QC completed!
[2024-01-24 13:27:07,494] [INFO] Total running time: 0h1m40s