[2024-01-24 13:46:25,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,668] [INFO] DQC Reference Directory: /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference
[2024-01-24 13:46:27,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,155] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,155] [INFO] Running command: gunzip -c /var/lib/cwl/stg05122e83-0538-4804-b64b-219dcfb349f3/GCF_021228795.1_ASM2122879v1_genomic.fna.gz | prodigal -d GCF_021228795.1_ASM2122879v1_genomic.fna/cds.fna -a GCF_021228795.1_ASM2122879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:46,137] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:46,137] [INFO] Task started: HMMsearch
[2024-01-24 13:46:46,137] [INFO] Running command: hmmsearch --tblout GCF_021228795.1_ASM2122879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/reference_markers.hmm GCF_021228795.1_ASM2122879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:46,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:46,501] [INFO] Found 6/6 markers.
[2024-01-24 13:46:46,550] [INFO] Query marker FASTA was written to GCF_021228795.1_ASM2122879v1_genomic.fna/markers.fasta
[2024-01-24 13:46:46,550] [INFO] Task started: Blastn
[2024-01-24 13:46:46,551] [INFO] Running command: blastn -query GCF_021228795.1_ASM2122879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/reference_markers.fasta -out GCF_021228795.1_ASM2122879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:47,491] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:47,494] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:47,495] [INFO] Target genome list was writen to GCF_021228795.1_ASM2122879v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:47,507] [INFO] Task started: fastANI
[2024-01-24 13:46:47,507] [INFO] Running command: fastANI --query /var/lib/cwl/stg05122e83-0538-4804-b64b-219dcfb349f3/GCF_021228795.1_ASM2122879v1_genomic.fna.gz --refList GCF_021228795.1_ASM2122879v1_genomic.fna/target_genomes.txt --output GCF_021228795.1_ASM2122879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:02,466] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:02,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:02,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:02,478] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:02,478] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:02,478] [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
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	100.0	1883	1883	95	conclusive
Thiocapsa marina	strain=5811	GCA_000223985.2	244573	244573	type	True	89.3805	1372	1883	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	87.4219	1261	1883	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	87.1427	1272	1883	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	78.5698	484	1883	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	78.5541	413	1883	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	78.4264	434	1883	95	below_threshold
Thiocystis minor	strain=DSM 178	GCA_016653465.1	61597	61597	type	True	78.3446	448	1883	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.2489	470	1883	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	78.244	446	1883	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.6808	142	1883	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	76.088	113	1883	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.0382	115	1883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:02,480] [INFO] DFAST Taxonomy check result was written to GCF_021228795.1_ASM2122879v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:02,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:02,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:02,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/checkm_data
[2024-01-24 13:47:02,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:02,542] [INFO] Task started: CheckM
[2024-01-24 13:47:02,542] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021228795.1_ASM2122879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021228795.1_ASM2122879v1_genomic.fna/checkm_input GCF_021228795.1_ASM2122879v1_genomic.fna/checkm_result
[2024-01-24 13:47:55,152] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:55,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:55,172] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:55,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:55,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021228795.1_ASM2122879v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:55,173] [INFO] Task started: Blastn
[2024-01-24 13:47:55,173] [INFO] Running command: blastn -query GCF_021228795.1_ASM2122879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf959de91-12ed-4e96-872b-868989cd68df/dqc_reference/reference_markers_gtdb.fasta -out GCF_021228795.1_ASM2122879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:56,626] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:56,631] [INFO] Selected 7 target genomes.
[2024-01-24 13:47:56,631] [INFO] Target genome list was writen to GCF_021228795.1_ASM2122879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:56,636] [INFO] Task started: fastANI
[2024-01-24 13:47:56,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg05122e83-0538-4804-b64b-219dcfb349f3/GCF_021228795.1_ASM2122879v1_genomic.fna.gz --refList GCF_021228795.1_ASM2122879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021228795.1_ASM2122879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:07,445] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:07,453] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:48:07,453] [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_000223985.1	s__Thiocapsa marina	89.3973	1370	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390875.1	s__Thiocapsa sp011390875	87.6377	955	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	87.4288	1260	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399035.1	s__Thiocapsa sp018399035	87.3074	1210	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	99.92	99.89	0.99	0.99	3	-
GCF_003634315.1	s__Thiocapsa rosea	87.1216	1272	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423035.1	s__Thiocapsa sp002423035	86.8537	1036	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499735.1	s__Thiocapsa sp001499735	85.9337	1183	1883	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocapsa	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:07,454] [INFO] GTDB search result was written to GCF_021228795.1_ASM2122879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:07,455] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:07,461] [INFO] DFAST_QC result json was written to GCF_021228795.1_ASM2122879v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:07,462] [INFO] DFAST_QC completed!
[2024-01-24 13:48:07,462] [INFO] Total running time: 0h1m42s