[2024-01-24 14:21:46,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:46,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:46,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference
[2024-01-24 14:21:47,706] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:47,707] [INFO] Task started: Prodigal
[2024-01-24 14:21:47,707] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b39bd43-9a1c-49fd-a01e-3c026bb872d3/GCF_014201885.1_ASM1420188v1_genomic.fna.gz | prodigal -d GCF_014201885.1_ASM1420188v1_genomic.fna/cds.fna -a GCF_014201885.1_ASM1420188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:10,512] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:10,512] [INFO] Task started: HMMsearch
[2024-01-24 14:22:10,512] [INFO] Running command: hmmsearch --tblout GCF_014201885.1_ASM1420188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/reference_markers.hmm GCF_014201885.1_ASM1420188v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:10,778] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:10,779] [INFO] Found 6/6 markers.
[2024-01-24 14:22:10,817] [INFO] Query marker FASTA was written to GCF_014201885.1_ASM1420188v1_genomic.fna/markers.fasta
[2024-01-24 14:22:10,818] [INFO] Task started: Blastn
[2024-01-24 14:22:10,818] [INFO] Running command: blastn -query GCF_014201885.1_ASM1420188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/reference_markers.fasta -out GCF_014201885.1_ASM1420188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:11,564] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:11,578] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:11,579] [INFO] Target genome list was writen to GCF_014201885.1_ASM1420188v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:11,584] [INFO] Task started: fastANI
[2024-01-24 14:22:11,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b39bd43-9a1c-49fd-a01e-3c026bb872d3/GCF_014201885.1_ASM1420188v1_genomic.fna.gz --refList GCF_014201885.1_ASM1420188v1_genomic.fna/target_genomes.txt --output GCF_014201885.1_ASM1420188v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:19,888] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:19,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:19,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:19,898] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:19,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:19,898] [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 budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	100.0	1258	1259	95	conclusive
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	84.5247	782	1259	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	83.2954	783	1259	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	82.9484	860	1259	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	82.7753	799	1259	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	82.7627	811	1259	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	82.6922	819	1259	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	82.4077	782	1259	95	below_threshold
Deinococcus aerophilus	strain=JCM 15443	GCA_014647075.1	522488	522488	type	True	80.2119	605	1259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:19,900] [INFO] DFAST Taxonomy check result was written to GCF_014201885.1_ASM1420188v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:19,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:19,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:19,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/checkm_data
[2024-01-24 14:22:19,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:19,968] [INFO] Task started: CheckM
[2024-01-24 14:22:19,968] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201885.1_ASM1420188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201885.1_ASM1420188v1_genomic.fna/checkm_input GCF_014201885.1_ASM1420188v1_genomic.fna/checkm_result
[2024-01-24 14:23:18,016] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:18,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:18,041] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:18,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:18,042] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201885.1_ASM1420188v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:18,042] [INFO] Task started: Blastn
[2024-01-24 14:23:18,042] [INFO] Running command: blastn -query GCF_014201885.1_ASM1420188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d7d2ee-7480-4e13-9cfd-caef013117e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201885.1_ASM1420188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:19,086] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:19,090] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:19,090] [INFO] Target genome list was writen to GCF_014201885.1_ASM1420188v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:19,099] [INFO] Task started: fastANI
[2024-01-24 14:23:19,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b39bd43-9a1c-49fd-a01e-3c026bb872d3/GCF_014201885.1_ASM1420188v1_genomic.fna.gz --refList GCF_014201885.1_ASM1420188v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201885.1_ASM1420188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:31,420] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:31,431] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:31,432] [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_014201885.1	s__Deinococcus budaensis	100.0	1258	1259	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_002953415.1	s__Deinococcus sp002953415	84.669	804	1259	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	84.5278	781	1259	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	83.2767	785	1259	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897375.1	s__Deinococcus aerius	82.9498	862	1259	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	82.7423	813	1259	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_000381345.1	s__Deinococcus apachensis	82.5843	802	1259	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	82.4324	833	1259	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869765.1	s__Deinococcus planocerae	82.4146	782	1259	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901445.1	s__Deinococcus koreensis	80.2642	723	1259	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001949125.1	s__Deinococcus marmoris_A	78.9999	605	1259	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 14:23:31,437] [INFO] GTDB search result was written to GCF_014201885.1_ASM1420188v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:31,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:31,447] [INFO] DFAST_QC result json was written to GCF_014201885.1_ASM1420188v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:31,447] [INFO] DFAST_QC completed!
[2024-01-24 14:23:31,447] [INFO] Total running time: 0h1m45s