[2024-01-24 13:40:40,071] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:40,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:40,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference
[2024-01-24 13:40:41,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:41,301] [INFO] Task started: Prodigal
[2024-01-24 13:40:41,301] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbb78034-0c08-41ab-b8a4-37ba62c83fc7/GCF_006980705.1_ASM698070v1_genomic.fna.gz | prodigal -d GCF_006980705.1_ASM698070v1_genomic.fna/cds.fna -a GCF_006980705.1_ASM698070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:48,578] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:48,579] [INFO] Task started: HMMsearch
[2024-01-24 13:40:48,579] [INFO] Running command: hmmsearch --tblout GCF_006980705.1_ASM698070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/reference_markers.hmm GCF_006980705.1_ASM698070v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,818] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,845] [INFO] Query marker FASTA was written to GCF_006980705.1_ASM698070v1_genomic.fna/markers.fasta
[2024-01-24 13:40:48,845] [INFO] Task started: Blastn
[2024-01-24 13:40:48,845] [INFO] Running command: blastn -query GCF_006980705.1_ASM698070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/reference_markers.fasta -out GCF_006980705.1_ASM698070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,659] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,662] [INFO] Selected 7 target genomes.
[2024-01-24 13:40:49,663] [INFO] Target genome list was writen to GCF_006980705.1_ASM698070v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,756] [INFO] Task started: fastANI
[2024-01-24 13:40:49,756] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb78034-0c08-41ab-b8a4-37ba62c83fc7/GCF_006980705.1_ASM698070v1_genomic.fna.gz --refList GCF_006980705.1_ASM698070v1_genomic.fna/target_genomes.txt --output GCF_006980705.1_ASM698070v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:54,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:54,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:54,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:54,419] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:54,419] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:40:54,419] [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
Tepidiphilus olei	strain=J18	GCA_006980705.1	2502184	2502184	type	True	100.0	756	761	95	inconclusive
Tepidiphilus baoligensis	strain=B18-69	GCA_012911495.1	2698687	2698687	type	True	96.9079	641	761	95	inconclusive
Tepidiphilus margaritifer	strain=DSM 15129	GCA_000425565.1	203471	203471	type	True	91.4174	587	761	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001418245.1	876478	876478	suspected-type	True	89.2385	591	761	95	below_threshold
Tepidiphilus thermophilus	strain=JCM 19170	GCA_001517365.1	876478	876478	suspected-type	True	89.2385	591	761	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	76.0653	121	761	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	75.9568	110	761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:54,421] [INFO] DFAST Taxonomy check result was written to GCF_006980705.1_ASM698070v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:54,422] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:54,422] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:54,422] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/checkm_data
[2024-01-24 13:40:54,423] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:54,452] [INFO] Task started: CheckM
[2024-01-24 13:40:54,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006980705.1_ASM698070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006980705.1_ASM698070v1_genomic.fna/checkm_input GCF_006980705.1_ASM698070v1_genomic.fna/checkm_result
[2024-01-24 13:41:21,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:21,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:21,257] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:21,257] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:21,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006980705.1_ASM698070v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:21,258] [INFO] Task started: Blastn
[2024-01-24 13:41:21,258] [INFO] Running command: blastn -query GCF_006980705.1_ASM698070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10705a20-8c0d-48a3-a4c6-2001bf5d0816/dqc_reference/reference_markers_gtdb.fasta -out GCF_006980705.1_ASM698070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,736] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,740] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:22,740] [INFO] Target genome list was writen to GCF_006980705.1_ASM698070v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:22,886] [INFO] Task started: fastANI
[2024-01-24 13:41:22,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb78034-0c08-41ab-b8a4-37ba62c83fc7/GCF_006980705.1_ASM698070v1_genomic.fna.gz --refList GCF_006980705.1_ASM698070v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006980705.1_ASM698070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:28,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:28,820] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:28,821] [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_012911495.1	s__Tepidiphilus baoligensis	96.9079	641	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	97.01	96.91	0.89	0.87	3	conclusive
GCF_000425565.1	s__Tepidiphilus margaritifer	91.4104	588	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006503695.1	s__Tepidiphilus succinatimandens	89.2432	589	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	98.86	98.78	0.95	0.95	4	-
GCA_016235745.1	s__Tepidiphilus sp016235745	87.5816	523	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Tepidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034845.1	s__Thauera_A sp003034845	77.8409	243	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001922305.1	s__Thauera chlorobenzoica	77.6983	230	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	97.93	95.88	0.91	0.86	3	-
GCA_003963015.1	s__Thauera sp003963015	77.6783	256	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911595.1	s__Azoarcus_D sp013911595	77.4359	127	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azoarcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007556595.1	s__Tepidimonas alkaliphilus	77.0953	122	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Tepidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720685.1	s__Zoogloea sp016720685	76.7094	156	761	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Zoogloea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,823] [INFO] GTDB search result was written to GCF_006980705.1_ASM698070v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:28,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:28,826] [INFO] DFAST_QC result json was written to GCF_006980705.1_ASM698070v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:28,827] [INFO] DFAST_QC completed!
[2024-01-24 13:41:28,827] [INFO] Total running time: 0h0m49s