[2024-01-24 13:36:56,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:56,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:56,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference
[2024-01-24 13:36:58,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:58,263] [INFO] Task started: Prodigal
[2024-01-24 13:36:58,263] [INFO] Running command: gunzip -c /var/lib/cwl/stg348e8f1c-6d45-4ad0-bb93-71f5441d2c84/GCF_013385175.1_ASM1338517v1_genomic.fna.gz | prodigal -d GCF_013385175.1_ASM1338517v1_genomic.fna/cds.fna -a GCF_013385175.1_ASM1338517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:11,766] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:11,767] [INFO] Task started: HMMsearch
[2024-01-24 13:37:11,767] [INFO] Running command: hmmsearch --tblout GCF_013385175.1_ASM1338517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/reference_markers.hmm GCF_013385175.1_ASM1338517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:12,104] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:12,107] [INFO] Found 6/6 markers.
[2024-01-24 13:37:12,146] [INFO] Query marker FASTA was written to GCF_013385175.1_ASM1338517v1_genomic.fna/markers.fasta
[2024-01-24 13:37:12,146] [INFO] Task started: Blastn
[2024-01-24 13:37:12,146] [INFO] Running command: blastn -query GCF_013385175.1_ASM1338517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/reference_markers.fasta -out GCF_013385175.1_ASM1338517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:13,137] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:13,140] [INFO] Selected 15 target genomes.
[2024-01-24 13:37:13,140] [INFO] Target genome list was writen to GCF_013385175.1_ASM1338517v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:13,149] [INFO] Task started: fastANI
[2024-01-24 13:37:13,149] [INFO] Running command: fastANI --query /var/lib/cwl/stg348e8f1c-6d45-4ad0-bb93-71f5441d2c84/GCF_013385175.1_ASM1338517v1_genomic.fna.gz --refList GCF_013385175.1_ASM1338517v1_genomic.fna/target_genomes.txt --output GCF_013385175.1_ASM1338517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:27,272] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:27,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:27,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:27,286] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:27,286] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:27,287] [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
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	100.0	1496	1497	95	conclusive
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	92.5541	979	1497	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	92.4701	937	1497	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	81.1525	756	1497	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	80.3105	596	1497	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	79.6293	612	1497	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	79.5883	603	1497	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	79.4602	593	1497	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	79.2827	363	1497	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.7035	490	1497	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	78.5331	429	1497	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	78.4432	395	1497	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5323	191	1497	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.3813	128	1497	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.3121	131	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,288] [INFO] DFAST Taxonomy check result was written to GCF_013385175.1_ASM1338517v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:27,289] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:27,289] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:27,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/checkm_data
[2024-01-24 13:37:27,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:27,355] [INFO] Task started: CheckM
[2024-01-24 13:37:27,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013385175.1_ASM1338517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013385175.1_ASM1338517v1_genomic.fna/checkm_input GCF_013385175.1_ASM1338517v1_genomic.fna/checkm_result
[2024-01-24 13:38:13,190] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:13,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,213] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:13,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:13,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013385175.1_ASM1338517v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:13,215] [INFO] Task started: Blastn
[2024-01-24 13:38:13,215] [INFO] Running command: blastn -query GCF_013385175.1_ASM1338517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40a24135-003f-42e7-a279-646a0eb813eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013385175.1_ASM1338517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:14,751] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:14,755] [INFO] Selected 10 target genomes.
[2024-01-24 13:38:14,756] [INFO] Target genome list was writen to GCF_013385175.1_ASM1338517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:14,809] [INFO] Task started: fastANI
[2024-01-24 13:38:14,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg348e8f1c-6d45-4ad0-bb93-71f5441d2c84/GCF_013385175.1_ASM1338517v1_genomic.fna.gz --refList GCF_013385175.1_ASM1338517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013385175.1_ASM1338517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:24,431] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:24,440] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:24,441] [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_013385175.1	s__Allochromatium humboldtianum	100.0	1496	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000025485.1	s__Allochromatium vinosum	92.5738	977	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_018409545.1	s__Allochromatium tepidum	92.5124	934	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720725.1	s__Allochromatium palmeri	87.9967	955	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009664085.1	s__Thermochromatium tepidum	85.9704	793	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thermochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	81.1576	756	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224065.1	s__Imhoffiella drewsii	79.6135	602	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Imhoffiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107145.1	s__Allochromatium warmingii	79.2858	361	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	78.8755	495	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCA_016192835.1	s__PALSA-1004 sp016192835	75.7046	70	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SG8-41;g__PALSA-1004	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:24,442] [INFO] GTDB search result was written to GCF_013385175.1_ASM1338517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:24,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:24,446] [INFO] DFAST_QC result json was written to GCF_013385175.1_ASM1338517v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:24,446] [INFO] DFAST_QC completed!
[2024-01-24 13:38:24,447] [INFO] Total running time: 0h1m28s