[2024-01-24 12:30:33,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:33,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:33,648] [INFO] DQC Reference Directory: /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference
[2024-01-24 12:30:34,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:34,866] [INFO] Task started: Prodigal
[2024-01-24 12:30:34,866] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcaa9c4e-8736-4feb-aeb4-98ed31a9853b/GCF_002091475.1_ASM209147v1_genomic.fna.gz | prodigal -d GCF_002091475.1_ASM209147v1_genomic.fna/cds.fna -a GCF_002091475.1_ASM209147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:49,152] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:49,153] [INFO] Task started: HMMsearch
[2024-01-24 12:30:49,153] [INFO] Running command: hmmsearch --tblout GCF_002091475.1_ASM209147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/reference_markers.hmm GCF_002091475.1_ASM209147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:49,453] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:49,455] [INFO] Found 6/6 markers.
[2024-01-24 12:30:49,502] [INFO] Query marker FASTA was written to GCF_002091475.1_ASM209147v1_genomic.fna/markers.fasta
[2024-01-24 12:30:49,503] [INFO] Task started: Blastn
[2024-01-24 12:30:49,503] [INFO] Running command: blastn -query GCF_002091475.1_ASM209147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/reference_markers.fasta -out GCF_002091475.1_ASM209147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:50,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:50,570] [INFO] Selected 13 target genomes.
[2024-01-24 12:30:50,571] [INFO] Target genome list was writen to GCF_002091475.1_ASM209147v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:50,613] [INFO] Task started: fastANI
[2024-01-24 12:30:50,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcaa9c4e-8736-4feb-aeb4-98ed31a9853b/GCF_002091475.1_ASM209147v1_genomic.fna.gz --refList GCF_002091475.1_ASM209147v1_genomic.fna/target_genomes.txt --output GCF_002091475.1_ASM209147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:04,568] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:04,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:04,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:04,581] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:04,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:04,582] [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 azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	100.0	1631	1639	95	conclusive
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	89.4348	1049	1639	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	88.3367	1062	1639	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	86.4965	992	1639	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	82.0081	757	1639	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	81.8492	831	1639	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	81.8442	778	1639	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	80.6159	737	1639	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	80.286	624	1639	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.6999	624	1639	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.5757	636	1639	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.445	599	1639	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.9149	567	1639	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:04,587] [INFO] DFAST Taxonomy check result was written to GCF_002091475.1_ASM209147v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:04,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:04,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:04,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/checkm_data
[2024-01-24 12:31:04,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:04,645] [INFO] Task started: CheckM
[2024-01-24 12:31:04,645] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002091475.1_ASM209147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002091475.1_ASM209147v1_genomic.fna/checkm_input GCF_002091475.1_ASM209147v1_genomic.fna/checkm_result
[2024-01-24 12:31:48,401] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:48,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:48,427] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:48,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:48,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002091475.1_ASM209147v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:48,428] [INFO] Task started: Blastn
[2024-01-24 12:31:48,428] [INFO] Running command: blastn -query GCF_002091475.1_ASM209147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc22459d1-c6d3-46ec-9db5-faaf375bb093/dqc_reference/reference_markers_gtdb.fasta -out GCF_002091475.1_ASM209147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:50,531] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:50,536] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:50,536] [INFO] Target genome list was writen to GCF_002091475.1_ASM209147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:50,546] [INFO] Task started: fastANI
[2024-01-24 12:31:50,547] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcaa9c4e-8736-4feb-aeb4-98ed31a9853b/GCF_002091475.1_ASM209147v1_genomic.fna.gz --refList GCF_002091475.1_ASM209147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002091475.1_ASM209147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:02,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:02,730] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:02,730] [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_002091475.1	s__Sphingomonas azotifigens	100.0	1631	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011927635.1	s__Sphingomonas trueperi	89.4205	1050	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_900114095.1	s__Sphingomonas sp900114095	89.2065	1118	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716975.1	s__Sphingomonas trueperi_A	89.0146	1122	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.23	95.23	0.88	0.88	2	-
GCF_012650175.1	s__Sphingomonas sp012650175	88.5619	998	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598435.1	s__Sphingomonas pituitosa	88.3355	1063	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650735.1	s__Sphingomonas sp001650735	88.2213	1162	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226955.1	s__Sphingomonas elodea_A	88.0617	1001	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096275.1	s__Sphingomonas pokkalii	86.4795	994	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282895.1	s__Sphingomonas sp000282895	85.6224	918	1639	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:02,732] [INFO] GTDB search result was written to GCF_002091475.1_ASM209147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:02,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:02,736] [INFO] DFAST_QC result json was written to GCF_002091475.1_ASM209147v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:02,736] [INFO] DFAST_QC completed!
[2024-01-24 12:32:02,736] [INFO] Total running time: 0h1m29s