[2024-01-24 10:57:07,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,323] [INFO] DQC Reference Directory: /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference
[2024-01-24 10:57:08,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,554] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg40f5d5fe-0ebc-484e-9aa7-db97adb59418/GCF_030161515.1_ASM3016151v1_genomic.fna.gz | prodigal -d GCF_030161515.1_ASM3016151v1_genomic.fna/cds.fna -a GCF_030161515.1_ASM3016151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:20,867] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:20,868] [INFO] Task started: HMMsearch
[2024-01-24 10:57:20,868] [INFO] Running command: hmmsearch --tblout GCF_030161515.1_ASM3016151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/reference_markers.hmm GCF_030161515.1_ASM3016151v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:21,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:21,141] [INFO] Found 6/6 markers.
[2024-01-24 10:57:21,180] [INFO] Query marker FASTA was written to GCF_030161515.1_ASM3016151v1_genomic.fna/markers.fasta
[2024-01-24 10:57:21,181] [INFO] Task started: Blastn
[2024-01-24 10:57:21,181] [INFO] Running command: blastn -query GCF_030161515.1_ASM3016151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/reference_markers.fasta -out GCF_030161515.1_ASM3016151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:21,845] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:21,849] [INFO] Selected 9 target genomes.
[2024-01-24 10:57:21,850] [INFO] Target genome list was writen to GCF_030161515.1_ASM3016151v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:21,854] [INFO] Task started: fastANI
[2024-01-24 10:57:21,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f5d5fe-0ebc-484e-9aa7-db97adb59418/GCF_030161515.1_ASM3016151v1_genomic.fna.gz --refList GCF_030161515.1_ASM3016151v1_genomic.fna/target_genomes.txt --output GCF_030161515.1_ASM3016151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:32,113] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:32,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:32,115] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:32,130] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:57:32,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:32,130] [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 metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	99.9973	1423	1447	95	conclusive
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	99.9963	1435	1447	95	conclusive
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	99.969	1297	1447	95	conclusive
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	86.1805	885	1447	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	85.5343	989	1447	95	below_threshold
Deinococcus geothermalis	strain=DSM 11300	GCA_000196275.1	68909	68909	type	True	83.742	779	1447	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	83.2414	840	1447	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	82.9134	852	1447	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	82.6515	813	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:32,132] [INFO] DFAST Taxonomy check result was written to GCF_030161515.1_ASM3016151v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:32,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:32,133] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:32,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/checkm_data
[2024-01-24 10:57:32,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:32,181] [INFO] Task started: CheckM
[2024-01-24 10:57:32,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030161515.1_ASM3016151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030161515.1_ASM3016151v1_genomic.fna/checkm_input GCF_030161515.1_ASM3016151v1_genomic.fna/checkm_result
[2024-01-24 10:58:11,854] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:11,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:11,874] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:11,875] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:11,875] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030161515.1_ASM3016151v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:11,876] [INFO] Task started: Blastn
[2024-01-24 10:58:11,876] [INFO] Running command: blastn -query GCF_030161515.1_ASM3016151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38d18769-b2b4-43b1-95d7-196fb0a33c85/dqc_reference/reference_markers_gtdb.fasta -out GCF_030161515.1_ASM3016151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:12,828] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:12,832] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:12,832] [INFO] Target genome list was writen to GCF_030161515.1_ASM3016151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:12,843] [INFO] Task started: fastANI
[2024-01-24 10:58:12,844] [INFO] Running command: fastANI --query /var/lib/cwl/stg40f5d5fe-0ebc-484e-9aa7-db97adb59418/GCF_030161515.1_ASM3016151v1_genomic.fna.gz --refList GCF_030161515.1_ASM3016151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030161515.1_ASM3016151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:24,887] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:24,907] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:24,908] [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_004758605.1	s__Deinococcus metallilatus	99.9973	1423	1447	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	conclusive
GCF_000599865.1	s__Deinococcus phoenicis	86.1637	887	1447	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	85.5544	987	1447	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196275.1	s__Deinococcus geothermalis	83.757	777	1447	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.28	97.91	0.91	0.89	4	-
GCF_002869765.1	s__Deinococcus planocerae	83.2468	839	1447	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381345.1	s__Deinococcus apachensis	82.9334	848	1447	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	82.7044	808	1447	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	82.5718	867	1447	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953415.1	s__Deinococcus sp002953415	82.0799	720	1447	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	81.7176	722	1447	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	79.7115	678	1447	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	79.0369	627	1447	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 10:58:24,910] [INFO] GTDB search result was written to GCF_030161515.1_ASM3016151v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:24,910] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:24,914] [INFO] DFAST_QC result json was written to GCF_030161515.1_ASM3016151v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:24,915] [INFO] DFAST_QC completed!
[2024-01-24 10:58:24,915] [INFO] Total running time: 0h1m18s