[2024-01-24 13:19:28,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:28,028] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:28,028] [INFO] DQC Reference Directory: /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference
[2024-01-24 13:19:29,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:29,396] [INFO] Task started: Prodigal
[2024-01-24 13:19:29,397] [INFO] Running command: gunzip -c /var/lib/cwl/stg0503dd45-4dcb-4480-bdd2-a171da95eeea/GCF_009664085.1_ASM966408v1_genomic.fna.gz | prodigal -d GCF_009664085.1_ASM966408v1_genomic.fna/cds.fna -a GCF_009664085.1_ASM966408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:38,713] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:38,713] [INFO] Task started: HMMsearch
[2024-01-24 13:19:38,713] [INFO] Running command: hmmsearch --tblout GCF_009664085.1_ASM966408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/reference_markers.hmm GCF_009664085.1_ASM966408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:38,971] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:38,972] [INFO] Found 6/6 markers.
[2024-01-24 13:19:39,003] [INFO] Query marker FASTA was written to GCF_009664085.1_ASM966408v1_genomic.fna/markers.fasta
[2024-01-24 13:19:39,004] [INFO] Task started: Blastn
[2024-01-24 13:19:39,004] [INFO] Running command: blastn -query GCF_009664085.1_ASM966408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/reference_markers.fasta -out GCF_009664085.1_ASM966408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:39,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:39,770] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:39,771] [INFO] Target genome list was writen to GCF_009664085.1_ASM966408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:39,788] [INFO] Task started: fastANI
[2024-01-24 13:19:39,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg0503dd45-4dcb-4480-bdd2-a171da95eeea/GCF_009664085.1_ASM966408v1_genomic.fna.gz --refList GCF_009664085.1_ASM966408v1_genomic.fna/target_genomes.txt --output GCF_009664085.1_ASM966408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:54,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:54,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:54,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:54,085] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:54,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:54,085] [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 tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	86.3334	803	986	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	86.0066	798	986	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	85.4891	748	986	95	below_threshold
Thiocystis violacea	strain=DSM 207	GCA_016583575.1	13725	13725	type	True	79.1817	518	986	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	78.8757	454	986	95	below_threshold
Marichromatium purpuratum	strain=984	GCA_000224005.3	37487	37487	type	True	78.8702	433	986	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	78.442	410	986	95	below_threshold
Allochromatium warmingii	strain=DSM 173	GCA_900107145.1	61595	61595	type	True	78.3222	229	986	95	below_threshold
Caldichromatium japonicum	strain=No.7	GCA_011290485.1	2699430	2699430	type	True	78.2208	411	986	95	below_threshold
Thiocapsa rosea	strain=DSM 235	GCA_003634315.1	69360	69360	type	True	78.1044	323	986	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	78.0057	316	986	95	below_threshold
Thiocapsa bogorovii	strain=BBS	GCA_021228795.1	521689	521689	type	True	77.9263	291	986	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.8135	236	986	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	76.6519	74	986	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.6469	85	986	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.5092	87	986	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.6769	79	986	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:54,087] [INFO] DFAST Taxonomy check result was written to GCF_009664085.1_ASM966408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:54,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:54,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:54,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/checkm_data
[2024-01-24 13:19:54,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:54,122] [INFO] Task started: CheckM
[2024-01-24 13:19:54,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009664085.1_ASM966408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009664085.1_ASM966408v1_genomic.fna/checkm_input GCF_009664085.1_ASM966408v1_genomic.fna/checkm_result
[2024-01-24 13:20:24,633] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:24,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:24,654] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:24,654] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:24,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009664085.1_ASM966408v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:24,655] [INFO] Task started: Blastn
[2024-01-24 13:20:24,655] [INFO] Running command: blastn -query GCF_009664085.1_ASM966408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg874b7492-2c3a-47e7-88bf-e16816c274fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_009664085.1_ASM966408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:25,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:25,748] [INFO] Selected 8 target genomes.
[2024-01-24 13:20:25,748] [INFO] Target genome list was writen to GCF_009664085.1_ASM966408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:25,771] [INFO] Task started: fastANI
[2024-01-24 13:20:25,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg0503dd45-4dcb-4480-bdd2-a171da95eeea/GCF_009664085.1_ASM966408v1_genomic.fna.gz --refList GCF_009664085.1_ASM966408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009664085.1_ASM966408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:33,104] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:33,119] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:33,119] [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_009664085.1	s__Thermochromatium tepidum	100.0	985	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thermochromatium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018409545.1	s__Allochromatium tepidum	86.3298	805	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013385175.1	s__Allochromatium humboldtianum	86.0212	797	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025485.1	s__Allochromatium vinosum	85.5071	743	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	97.59	97.59	0.87	0.87	2	-
GCF_009720725.1	s__Allochromatium palmeri	83.3632	735	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583575.1	s__Thiocystis violacea	79.186	517	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107145.1	s__Allochromatium warmingii	78.3222	229	986	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Allochromatium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106925.1	s__Thiocapsa roseopersicina	78.0047	316	986	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 13:20:33,120] [INFO] GTDB search result was written to GCF_009664085.1_ASM966408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:33,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:33,124] [INFO] DFAST_QC result json was written to GCF_009664085.1_ASM966408v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:33,124] [INFO] DFAST_QC completed!
[2024-01-24 13:20:33,124] [INFO] Total running time: 0h1m5s