[2024-01-24 13:36:45,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,489] [INFO] DQC Reference Directory: /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference
[2024-01-24 13:36:46,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,866] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,866] [INFO] Running command: gunzip -c /var/lib/cwl/stga69c8a46-093c-4d6d-8842-61c40c0799a1/GCF_014875965.1_ASM1487596v1_genomic.fna.gz | prodigal -d GCF_014875965.1_ASM1487596v1_genomic.fna/cds.fna -a GCF_014875965.1_ASM1487596v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:56,838] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:56,839] [INFO] Task started: HMMsearch
[2024-01-24 13:36:56,839] [INFO] Running command: hmmsearch --tblout GCF_014875965.1_ASM1487596v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/reference_markers.hmm GCF_014875965.1_ASM1487596v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:57,066] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:57,067] [INFO] Found 6/6 markers.
[2024-01-24 13:36:57,097] [INFO] Query marker FASTA was written to GCF_014875965.1_ASM1487596v1_genomic.fna/markers.fasta
[2024-01-24 13:36:57,097] [INFO] Task started: Blastn
[2024-01-24 13:36:57,097] [INFO] Running command: blastn -query GCF_014875965.1_ASM1487596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/reference_markers.fasta -out GCF_014875965.1_ASM1487596v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:57,752] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:57,755] [INFO] Selected 6 target genomes.
[2024-01-24 13:36:57,755] [INFO] Target genome list was writen to GCF_014875965.1_ASM1487596v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:57,760] [INFO] Task started: fastANI
[2024-01-24 13:36:57,760] [INFO] Running command: fastANI --query /var/lib/cwl/stga69c8a46-093c-4d6d-8842-61c40c0799a1/GCF_014875965.1_ASM1487596v1_genomic.fna.gz --refList GCF_014875965.1_ASM1487596v1_genomic.fna/target_genomes.txt --output GCF_014875965.1_ASM1487596v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:53,393] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:53,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:53,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:53,400] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 13:38:53,400] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:53,400] [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 wulumuqiensis	strain=R12	GCA_014875845.1	980427	980427	type	True	99.9692	1045	1111	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875745.1	980427	980427	type	True	99.9249	1016	1111	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875835.1	980427	980427	type	True	99.9156	980	1111	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875975.1	980427	980427	type	True	99.9012	1004	1111	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_000348665.1	980427	980427	type	True	99.8795	961	1111	95	conclusive
Deinococcus wulumuqiensis	strain=R12	GCA_014875875.1	980427	980427	type	True	99.8083	983	1111	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:38:53,402] [INFO] DFAST Taxonomy check result was written to GCF_014875965.1_ASM1487596v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:53,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:53,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:53,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/checkm_data
[2024-01-24 13:38:53,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:53,439] [INFO] Task started: CheckM
[2024-01-24 13:38:53,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014875965.1_ASM1487596v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014875965.1_ASM1487596v1_genomic.fna/checkm_input GCF_014875965.1_ASM1487596v1_genomic.fna/checkm_result
[2024-01-24 13:39:25,289] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:25,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:25,311] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:25,311] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:25,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014875965.1_ASM1487596v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:25,311] [INFO] Task started: Blastn
[2024-01-24 13:39:25,312] [INFO] Running command: blastn -query GCF_014875965.1_ASM1487596v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83a3d366-620d-44b8-9d2b-e4af925bbfe3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014875965.1_ASM1487596v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:26,263] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:26,267] [INFO] Selected 18 target genomes.
[2024-01-24 13:39:26,267] [INFO] Target genome list was writen to GCF_014875965.1_ASM1487596v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:26,293] [INFO] Task started: fastANI
[2024-01-24 13:39:26,294] [INFO] Running command: fastANI --query /var/lib/cwl/stga69c8a46-093c-4d6d-8842-61c40c0799a1/GCF_014875965.1_ASM1487596v1_genomic.fna.gz --refList GCF_014875965.1_ASM1487596v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014875965.1_ASM1487596v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:44,942] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:44,957] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:44,957] [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_011067105.1	s__Deinococcus wulumuqiensis	99.9692	1045	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.82	97.50	0.97	0.83	19	conclusive
GCF_000008565.1	s__Deinococcus radiodurans	87.4492	811	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	99.94	99.91	0.99	0.99	8	-
GCF_900109185.1	s__Deinococcus reticulitermitis	80.8066	651	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252445.1	s__Deinococcus gobiensis	80.6498	600	1111	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	79.8414	542	1111	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	79.7665	535	1111	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	79.7576	573	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260275.1	s__Deinococcus sp018260275	79.7295	350	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018260405.1	s__Deinococcus sp018260405	79.4416	417	1111	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	79.3552	544	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	100.00	100.00	0.98	0.98	4	-
GCF_014647075.1	s__Deinococcus aerophilus	79.2794	513	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003444775.1	s__Deinococcus ficus	79.2022	471	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.33	97.44	0.95	0.88	4	-
GCF_013337115.1	s__Deinococcus sp013337115	78.9559	488	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190555.1	s__Deinococcus proteolyticus	78.9344	378	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485435.1	s__Deinococcus grandis	78.9266	512	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	96.65	95.40	0.88	0.83	5	-
GCF_001007995.1	s__Deinococcus soli	78.8731	469	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	98.09	98.03	0.94	0.93	3	-
GCF_000701425.1	s__Deinococcus frigens	78.8231	490	1111	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Deinococcaceae;g__Deinococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647435.1	s__Deinococcus radiotolerans	78.5768	466	1111	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 13:39:44,959] [INFO] GTDB search result was written to GCF_014875965.1_ASM1487596v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:44,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:44,963] [INFO] DFAST_QC result json was written to GCF_014875965.1_ASM1487596v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:44,964] [INFO] DFAST_QC completed!
[2024-01-24 13:39:44,964] [INFO] Total running time: 0h2m59s