[2024-01-25 18:58:50,668] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:50,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:50,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference
[2024-01-25 18:58:51,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:51,818] [INFO] Task started: Prodigal
[2024-01-25 18:58:51,819] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd075cb6-7bcb-48a8-aeba-feb0c9af6e83/GCF_001644565.1_ASM164456v1_genomic.fna.gz | prodigal -d GCF_001644565.1_ASM164456v1_genomic.fna/cds.fna -a GCF_001644565.1_ASM164456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:00,359] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:00,359] [INFO] Task started: HMMsearch
[2024-01-25 18:59:00,359] [INFO] Running command: hmmsearch --tblout GCF_001644565.1_ASM164456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/reference_markers.hmm GCF_001644565.1_ASM164456v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:00,571] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:00,572] [INFO] Found 6/6 markers.
[2024-01-25 18:59:00,597] [INFO] Query marker FASTA was written to GCF_001644565.1_ASM164456v1_genomic.fna/markers.fasta
[2024-01-25 18:59:00,598] [INFO] Task started: Blastn
[2024-01-25 18:59:00,598] [INFO] Running command: blastn -query GCF_001644565.1_ASM164456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/reference_markers.fasta -out GCF_001644565.1_ASM164456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:01,178] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:01,181] [INFO] Selected 20 target genomes.
[2024-01-25 18:59:01,181] [INFO] Target genome list was writen to GCF_001644565.1_ASM164456v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:01,192] [INFO] Task started: fastANI
[2024-01-25 18:59:01,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd075cb6-7bcb-48a8-aeba-feb0c9af6e83/GCF_001644565.1_ASM164456v1_genomic.fna.gz --refList GCF_001644565.1_ASM164456v1_genomic.fna/target_genomes.txt --output GCF_001644565.1_ASM164456v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:16,268] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:16,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:16,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:16,283] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:16,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:16,283] [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 puniceus	strain=DY1	GCA_001644565.1	1182568	1182568	type	True	100.0	990	990	95	conclusive
Deinococcus aquatilis	strain=DSM 23025	GCA_000378445.1	519440	519440	type	True	86.3885	860	990	95	below_threshold
Deinococcus phoenicis	strain=1P10ME	GCA_000599865.1	1476583	1476583	type	True	78.5647	435	990	95	below_threshold
Deinococcus marmoris	strain=DSM 12784	GCA_000701405.1	249408	249408	type	True	78.3962	457	990	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	78.2532	424	990	95	below_threshold
Deinococcus multiflagellatus	strain=KACC 19287	GCA_020166415.1	1656887	1656887	type	True	78.1438	438	990	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	78.0709	410	990	95	below_threshold
Deinococcus arcticus	strain=OD32	GCA_003028415.1	2136176	2136176	type	True	78.0611	429	990	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	78.0138	418	990	95	below_threshold
Deinococcus radiodurans	strain=R1	GCA_000008565.1	1299	1299	type	True	77.998	343	990	95	below_threshold
Deinococcus radiodurans	strain=ATCC 13939	GCA_020546685.1	1299	1299	type	True	77.9831	349	990	95	below_threshold
Deinococcus budaensis	strain=DSM 101791	GCA_014201885.1	1665626	1665626	type	True	77.9521	426	990	95	below_threshold
Deinococcus radiodurans	strain=DSM 20539	GCA_000685985.1	1299	1299	type	True	77.8046	342	990	95	below_threshold
Deinococcus seoulensis	strain=JCM 31404	GCA_014648115.1	1837379	1837379	type	True	77.7918	413	990	95	below_threshold
Deinococcus knuensis	strain=JCM 31406	GCA_014648155.1	1837380	1837380	type	True	77.7489	424	990	95	below_threshold
Deinococcus humi	strain=DSM 27939	GCA_014201875.1	662880	662880	type	True	77.7348	384	990	95	below_threshold
Deinococcus humi	strain=JCM 17915	GCA_014647275.1	662880	662880	type	True	77.7049	382	990	95	below_threshold
Deinococcus xianganensis	strain=Y35	GCA_009834985.1	1507289	1507289	type	True	77.5961	363	990	95	below_threshold
Deinococcus fonticola	strain=FeSDHB5-19	GCA_004634215.1	2528713	2528713	type	True	77.5701	340	990	95	below_threshold
Deinococcus planocerae	strain=XY-FW106	GCA_002869765.1	1737569	1737569	type	True	77.2835	335	990	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:16,285] [INFO] DFAST Taxonomy check result was written to GCF_001644565.1_ASM164456v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:16,285] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:16,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:16,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/checkm_data
[2024-01-25 18:59:16,287] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:16,320] [INFO] Task started: CheckM
[2024-01-25 18:59:16,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001644565.1_ASM164456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001644565.1_ASM164456v1_genomic.fna/checkm_input GCF_001644565.1_ASM164456v1_genomic.fna/checkm_result
[2024-01-25 18:59:43,858] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:43,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:43,878] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:43,878] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:43,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001644565.1_ASM164456v1_genomic.fna/markers.fasta)
[2024-01-25 18:59:43,879] [INFO] Task started: Blastn
[2024-01-25 18:59:43,879] [INFO] Running command: blastn -query GCF_001644565.1_ASM164456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg990ec4a6-8f7d-44bd-b5d3-4a3428050ef2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001644565.1_ASM164456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:44,660] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:44,663] [INFO] Selected 15 target genomes.
[2024-01-25 18:59:44,663] [INFO] Target genome list was writen to GCF_001644565.1_ASM164456v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:44,676] [INFO] Task started: fastANI
[2024-01-25 18:59:44,676] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd075cb6-7bcb-48a8-aeba-feb0c9af6e83/GCF_001644565.1_ASM164456v1_genomic.fna.gz --refList GCF_001644565.1_ASM164456v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001644565.1_ASM164456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:57,214] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:57,224] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:57,224] [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_001644565.1	s__Deinococcus puniceus	100.0	990	990	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_004801315.1	s__Deinococcus sp004801315	89.4687	722	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378445.1	s__Deinococcus aquatilis	86.3885	860	990	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	78.5656	435	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701405.1	s__Deinococcus marmoris	78.395	456	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335125.1	s__Deinococcus radiopugnans	78.3171	469	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.45	97.61	0.92	0.87	4	-
GCF_004758605.1	s__Deinococcus metallilatus	78.2274	428	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_003028415.1	s__Deinococcus sp003028415	78.067	429	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002017875.1	s__Deinococcus sp002017875	77.9773	423	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.85	96.85	0.84	0.84	2	-
GCF_013337115.1	s__Deinococcus sp013337115	77.963	386	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008565.1	s__Deinococcus radiodurans	77.9314	346	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_002198095.1	s__Deinococcus indicus	77.894	398	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.28	99.28	0.90	0.90	2	-
GCF_004634215.1	s__Deinococcus fonticola	77.5542	341	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.54	96.54	0.85	0.85	2	-
GCF_000196275.1	s__Deinococcus geothermalis	77.5235	287	990	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	77.2685	333	990	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:57,231] [INFO] GTDB search result was written to GCF_001644565.1_ASM164456v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:57,232] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:57,235] [INFO] DFAST_QC result json was written to GCF_001644565.1_ASM164456v1_genomic.fna/dqc_result.json
[2024-01-25 18:59:57,235] [INFO] DFAST_QC completed!
[2024-01-25 18:59:57,235] [INFO] Total running time: 0h1m7s