[2024-01-24 14:54:56,533] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,536] [INFO] DQC Reference Directory: /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference
[2024-01-24 14:54:57,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,935] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg2edbda87-8dbd-47a6-b68b-0b15dfcadd58/GCF_002869765.1_ASM286976v1_genomic.fna.gz | prodigal -d GCF_002869765.1_ASM286976v1_genomic.fna/cds.fna -a GCF_002869765.1_ASM286976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:09,558] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:09,559] [INFO] Task started: HMMsearch
[2024-01-24 14:55:09,559] [INFO] Running command: hmmsearch --tblout GCF_002869765.1_ASM286976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/reference_markers.hmm GCF_002869765.1_ASM286976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:09,871] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:09,873] [INFO] Found 6/6 markers.
[2024-01-24 14:55:09,921] [INFO] Query marker FASTA was written to GCF_002869765.1_ASM286976v1_genomic.fna/markers.fasta
[2024-01-24 14:55:09,921] [INFO] Task started: Blastn
[2024-01-24 14:55:09,922] [INFO] Running command: blastn -query GCF_002869765.1_ASM286976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/reference_markers.fasta -out GCF_002869765.1_ASM286976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:10,607] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:10,611] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:10,611] [INFO] Target genome list was writen to GCF_002869765.1_ASM286976v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:10,617] [INFO] Task started: fastANI
[2024-01-24 14:55:10,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edbda87-8dbd-47a6-b68b-0b15dfcadd58/GCF_002869765.1_ASM286976v1_genomic.fna.gz --refList GCF_002869765.1_ASM286976v1_genomic.fna/target_genomes.txt --output GCF_002869765.1_ASM286976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:22,069] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:22,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:22,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:22,081] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:22,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:22,081] [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 planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	100.0	1387	1392	95	conclusive
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	84.7167	949	1392	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	83.3069	823	1392	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	83.2238	847	1392	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	83.1187	845	1392	95	below_threshold
Deinococcus apachensis	strain=DSM 19763	GCA_000381345.1	309886	309886	type	True	82.8511	827	1392	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	82.3233	796	1392	95	below_threshold
Deinococcus terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	81.6808	703	1392	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	81.6807	748	1392	95	below_threshold
Deinococcus actinosclerus	strain=BM2	GCA_001507665.1	1768108	1768108	type	True	79.0941	567	1392	95	below_threshold
Deinococcus kurensis	strain=KR-1	GCA_009687825.1	2662757	2662757	type	True	78.9569	644	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:22,083] [INFO] DFAST Taxonomy check result was written to GCF_002869765.1_ASM286976v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:22,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:22,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:22,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/checkm_data
[2024-01-24 14:55:22,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:22,128] [INFO] Task started: CheckM
[2024-01-24 14:55:22,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002869765.1_ASM286976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002869765.1_ASM286976v1_genomic.fna/checkm_input GCF_002869765.1_ASM286976v1_genomic.fna/checkm_result
[2024-01-24 14:56:00,351] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:00,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,375] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:00,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:00,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002869765.1_ASM286976v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:00,376] [INFO] Task started: Blastn
[2024-01-24 14:56:00,376] [INFO] Running command: blastn -query GCF_002869765.1_ASM286976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddaa0def-1ef0-4ee7-9af6-26e8501ff003/dqc_reference/reference_markers_gtdb.fasta -out GCF_002869765.1_ASM286976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,344] [INFO] Selected 11 target genomes.
[2024-01-24 14:56:01,344] [INFO] Target genome list was writen to GCF_002869765.1_ASM286976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:01,354] [INFO] Task started: fastANI
[2024-01-24 14:56:01,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg2edbda87-8dbd-47a6-b68b-0b15dfcadd58/GCF_002869765.1_ASM286976v1_genomic.fna.gz --refList GCF_002869765.1_ASM286976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002869765.1_ASM286976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:12,330] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:12,347] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:12,348] [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_002869765.1	s__Deinococcus planocerae	100.0	1387	1392	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_018863415.1	s__Deinococcus sp018863415	90.8011	1093	1392	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	84.7487	946	1392	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	83.1842	852	1392	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	82.8605	826	1392	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	82.3476	794	1392	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	81.8453	724	1392	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	81.7002	746	1392	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	79.5085	642	1392	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507665.1	s__Deinococcus actinosclerus	79.1191	564	1392	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.26	96.21	0.94	0.94	4	-
GCF_001949125.1	s__Deinococcus marmoris_A	78.1023	509	1392	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 14:56:12,349] [INFO] GTDB search result was written to GCF_002869765.1_ASM286976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:12,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:12,353] [INFO] DFAST_QC result json was written to GCF_002869765.1_ASM286976v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:12,353] [INFO] DFAST_QC completed!
[2024-01-24 14:56:12,353] [INFO] Total running time: 0h1m16s