[2024-01-24 14:03:02,574] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:02,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:02,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference
[2024-01-24 14:03:03,815] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:03,816] [INFO] Task started: Prodigal
[2024-01-24 14:03:03,816] [INFO] Running command: gunzip -c /var/lib/cwl/stg59b1ef66-29c7-4754-baaf-d9d50001cab4/GCF_009377345.1_ASM937734v1_genomic.fna.gz | prodigal -d GCF_009377345.1_ASM937734v1_genomic.fna/cds.fna -a GCF_009377345.1_ASM937734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:24,186] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:24,186] [INFO] Task started: HMMsearch
[2024-01-24 14:03:24,186] [INFO] Running command: hmmsearch --tblout GCF_009377345.1_ASM937734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/reference_markers.hmm GCF_009377345.1_ASM937734v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:24,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:24,473] [INFO] Found 6/6 markers.
[2024-01-24 14:03:24,512] [INFO] Query marker FASTA was written to GCF_009377345.1_ASM937734v1_genomic.fna/markers.fasta
[2024-01-24 14:03:24,513] [INFO] Task started: Blastn
[2024-01-24 14:03:24,513] [INFO] Running command: blastn -query GCF_009377345.1_ASM937734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/reference_markers.fasta -out GCF_009377345.1_ASM937734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:25,264] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:25,267] [INFO] Selected 9 target genomes.
[2024-01-24 14:03:25,268] [INFO] Target genome list was writen to GCF_009377345.1_ASM937734v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:25,274] [INFO] Task started: fastANI
[2024-01-24 14:03:25,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b1ef66-29c7-4754-baaf-d9d50001cab4/GCF_009377345.1_ASM937734v1_genomic.fna.gz --refList GCF_009377345.1_ASM937734v1_genomic.fna/target_genomes.txt --output GCF_009377345.1_ASM937734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:33,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:33,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:33,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:33,864] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:33,864] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:33,865] [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 terrestris	strain=SDU3-2	GCA_009377345.1	2651870	2651870	type	True	100.0	1139	1145	95	conclusive
Deinococcus murrayi	strain=DSM 11303	GCA_000482805.1	68910	68910	type	True	85.923	736	1145	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	84.4526	791	1145	95	below_threshold
Deinococcus aerius	strain=TR0125	GCA_002897375.1	200253	200253	type	True	82.4545	736	1145	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	81.9433	685	1145	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	81.909	723	1145	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	81.8012	702	1145	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	79.1435	539	1145	95	below_threshold
Deinococcus malanensis	strain=JCM 30331	GCA_014647655.1	1706855	1706855	type	True	78.6111	407	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:33,866] [INFO] DFAST Taxonomy check result was written to GCF_009377345.1_ASM937734v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:33,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:33,867] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:33,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/checkm_data
[2024-01-24 14:03:33,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:33,905] [INFO] Task started: CheckM
[2024-01-24 14:03:33,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009377345.1_ASM937734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009377345.1_ASM937734v1_genomic.fna/checkm_input GCF_009377345.1_ASM937734v1_genomic.fna/checkm_result
[2024-01-24 14:04:29,224] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:29,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:29,244] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:29,244] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:29,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009377345.1_ASM937734v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:29,245] [INFO] Task started: Blastn
[2024-01-24 14:04:29,245] [INFO] Running command: blastn -query GCF_009377345.1_ASM937734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg935b4475-11c2-46e9-a3f7-c241dd7d6d1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009377345.1_ASM937734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:30,326] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:30,330] [INFO] Selected 7 target genomes.
[2024-01-24 14:04:30,331] [INFO] Target genome list was writen to GCF_009377345.1_ASM937734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:30,340] [INFO] Task started: fastANI
[2024-01-24 14:04:30,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg59b1ef66-29c7-4754-baaf-d9d50001cab4/GCF_009377345.1_ASM937734v1_genomic.fna.gz --refList GCF_009377345.1_ASM937734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009377345.1_ASM937734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:36,811] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:36,823] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:36,824] [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_009377345.1	s__Deinococcus sp009377345	100.0	1138	1145	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	90.7777	899	1145	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482805.1	s__Deinococcus murrayi	85.9344	735	1145	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	97.89	97.89	0.90	0.90	2	-
GCF_014201885.1	s__Deinococcus budaensis	84.4325	793	1145	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	82.4064	741	1145	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	81.9605	733	1145	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	81.9517	719	1145	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 14:04:36,826] [INFO] GTDB search result was written to GCF_009377345.1_ASM937734v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:36,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:36,833] [INFO] DFAST_QC result json was written to GCF_009377345.1_ASM937734v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:36,833] [INFO] DFAST_QC completed!
[2024-01-24 14:04:36,833] [INFO] Total running time: 0h1m34s