[2024-01-24 12:45:09,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:09,808] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:09,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference
[2024-01-24 12:45:13,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,085] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,085] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc3a04b4-7bd9-4da3-986a-084e4dcf1a27/GCF_014358075.1_ASM1435807v1_genomic.fna.gz | prodigal -d GCF_014358075.1_ASM1435807v1_genomic.fna/cds.fna -a GCF_014358075.1_ASM1435807v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:24,145] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:24,145] [INFO] Task started: HMMsearch
[2024-01-24 12:45:24,145] [INFO] Running command: hmmsearch --tblout GCF_014358075.1_ASM1435807v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/reference_markers.hmm GCF_014358075.1_ASM1435807v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:24,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:24,462] [INFO] Found 6/6 markers.
[2024-01-24 12:45:24,499] [INFO] Query marker FASTA was written to GCF_014358075.1_ASM1435807v1_genomic.fna/markers.fasta
[2024-01-24 12:45:24,500] [INFO] Task started: Blastn
[2024-01-24 12:45:24,500] [INFO] Running command: blastn -query GCF_014358075.1_ASM1435807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/reference_markers.fasta -out GCF_014358075.1_ASM1435807v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:25,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:25,501] [INFO] Selected 11 target genomes.
[2024-01-24 12:45:25,501] [INFO] Target genome list was writen to GCF_014358075.1_ASM1435807v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:25,506] [INFO] Task started: fastANI
[2024-01-24 12:45:25,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3a04b4-7bd9-4da3-986a-084e4dcf1a27/GCF_014358075.1_ASM1435807v1_genomic.fna.gz --refList GCF_014358075.1_ASM1435807v1_genomic.fna/target_genomes.txt --output GCF_014358075.1_ASM1435807v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:36,869] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:36,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:36,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:36,880] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:36,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:36,880] [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
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	100.0	1304	1308	95	conclusive
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	88.9791	919	1308	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	87.9105	936	1308	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	84.4013	805	1308	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	83.4369	741	1308	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	80.8495	685	1308	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.2167	580	1308	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.4222	596	1308	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	79.3181	486	1308	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.1213	519	1308	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.0084	524	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,886] [INFO] DFAST Taxonomy check result was written to GCF_014358075.1_ASM1435807v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:36,887] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:36,887] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:36,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/checkm_data
[2024-01-24 12:45:36,889] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:36,933] [INFO] Task started: CheckM
[2024-01-24 12:45:36,939] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014358075.1_ASM1435807v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014358075.1_ASM1435807v1_genomic.fna/checkm_input GCF_014358075.1_ASM1435807v1_genomic.fna/checkm_result
[2024-01-24 12:46:11,941] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:11,942] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:11,969] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:11,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:11,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014358075.1_ASM1435807v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:11,971] [INFO] Task started: Blastn
[2024-01-24 12:46:11,971] [INFO] Running command: blastn -query GCF_014358075.1_ASM1435807v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b895cee-3c6f-4470-b361-730e802202c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_014358075.1_ASM1435807v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:13,809] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:13,813] [INFO] Selected 15 target genomes.
[2024-01-24 12:46:13,813] [INFO] Target genome list was writen to GCF_014358075.1_ASM1435807v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:13,833] [INFO] Task started: fastANI
[2024-01-24 12:46:13,833] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3a04b4-7bd9-4da3-986a-084e4dcf1a27/GCF_014358075.1_ASM1435807v1_genomic.fna.gz --refList GCF_014358075.1_ASM1435807v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014358075.1_ASM1435807v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:30,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:30,534] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:30,534] [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_014358075.1	s__Sphingomonas albertensis	100.0	1304	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003240625.1	s__Sphingomonas taxi_A	94.4271	884	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004101245.1	s__Sphingomonas sp004101245	90.06	1019	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	89.3644	939	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
GCF_001421745.1	s__Sphingomonas sp001421745	89.058	898	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053745.1	s__Sphingomonas faeni	88.9635	920	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050745.1	s__Sphingomonas sp003050745	88.9518	907	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.19	95.12	0.89	0.88	3	-
GCF_004795835.1	s__Sphingomonas sp004795835	88.8972	899	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421415.1	s__Sphingomonas sp001421415	88.8875	914	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340965.1	s__Sphingomonas sp004340965	88.8214	919	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115295.1	s__Sphingomonas sp900115295	88.7772	954	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422045.1	s__Sphingomonas sp001422045	88.7656	904	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688595.1	s__Sphingomonas sp003688595	88.7284	889	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424005.1	s__Sphingomonas sp001424005	88.7195	899	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013374115.1	s__Sphingomonas sp013374115	87.7167	886	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:30,536] [INFO] GTDB search result was written to GCF_014358075.1_ASM1435807v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:30,536] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:30,540] [INFO] DFAST_QC result json was written to GCF_014358075.1_ASM1435807v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:30,540] [INFO] DFAST_QC completed!
[2024-01-24 12:46:30,540] [INFO] Total running time: 0h1m21s