[2024-01-24 13:21:11,122] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:11,124] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:11,124] [INFO] DQC Reference Directory: /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference
[2024-01-24 13:21:12,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,323] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0869c18-f0f4-4d4d-ac5d-fc47c9a42b0f/GCF_014199255.1_ASM1419925v1_genomic.fna.gz | prodigal -d GCF_014199255.1_ASM1419925v1_genomic.fna/cds.fna -a GCF_014199255.1_ASM1419925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:25,750] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:25,750] [INFO] Task started: HMMsearch
[2024-01-24 13:21:25,750] [INFO] Running command: hmmsearch --tblout GCF_014199255.1_ASM1419925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/reference_markers.hmm GCF_014199255.1_ASM1419925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:26,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:26,016] [INFO] Found 6/6 markers.
[2024-01-24 13:21:26,060] [INFO] Query marker FASTA was written to GCF_014199255.1_ASM1419925v1_genomic.fna/markers.fasta
[2024-01-24 13:21:26,061] [INFO] Task started: Blastn
[2024-01-24 13:21:26,061] [INFO] Running command: blastn -query GCF_014199255.1_ASM1419925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/reference_markers.fasta -out GCF_014199255.1_ASM1419925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:26,966] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:26,971] [INFO] Selected 17 target genomes.
[2024-01-24 13:21:26,972] [INFO] Target genome list was writen to GCF_014199255.1_ASM1419925v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:26,984] [INFO] Task started: fastANI
[2024-01-24 13:21:26,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0869c18-f0f4-4d4d-ac5d-fc47c9a42b0f/GCF_014199255.1_ASM1419925v1_genomic.fna.gz --refList GCF_014199255.1_ASM1419925v1_genomic.fna/target_genomes.txt --output GCF_014199255.1_ASM1419925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:41,221] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:41,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:41,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:41,234] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:41,235] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:41,235] [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 xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	100.0	1457	1458	95	conclusive
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.9843	683	1458	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.9668	688	1458	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	80.5755	661	1458	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	80.5703	660	1458	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	80.5152	647	1458	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.4487	617	1458	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	80.3496	671	1458	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	80.3426	623	1458	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	80.3078	664	1458	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	80.2791	644	1458	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.8379	506	1458	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.2549	453	1458	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.0234	466	1458	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.7391	435	1458	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.5905	448	1458	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	78.3802	341	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:41,236] [INFO] DFAST Taxonomy check result was written to GCF_014199255.1_ASM1419925v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:41,237] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:41,237] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:41,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/checkm_data
[2024-01-24 13:21:41,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:41,282] [INFO] Task started: CheckM
[2024-01-24 13:21:41,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199255.1_ASM1419925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199255.1_ASM1419925v1_genomic.fna/checkm_input GCF_014199255.1_ASM1419925v1_genomic.fna/checkm_result
[2024-01-24 13:22:24,995] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:24,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:25,017] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:25,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:25,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199255.1_ASM1419925v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:25,018] [INFO] Task started: Blastn
[2024-01-24 13:22:25,019] [INFO] Running command: blastn -query GCF_014199255.1_ASM1419925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38b50a70-bbe6-460a-9037-a8b27f7b52da/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199255.1_ASM1419925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:26,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:26,742] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:26,743] [INFO] Target genome list was writen to GCF_014199255.1_ASM1419925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:26,763] [INFO] Task started: fastANI
[2024-01-24 13:22:26,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0869c18-f0f4-4d4d-ac5d-fc47c9a42b0f/GCF_014199255.1_ASM1419925v1_genomic.fna.gz --refList GCF_014199255.1_ASM1419925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199255.1_ASM1419925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:44,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,940] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:44,940] [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_014199255.1	s__Sphingomonas xinjiangensis	100.0	1457	1458	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_002002925.1	s__Sphingomonas sp002002925	80.9981	677	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	80.982	686	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017744835.1	s__Sphingomonas sp017744835	80.9735	632	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	80.8403	649	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	80.8211	614	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	80.6486	628	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	80.5843	660	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	80.5702	660	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927635.1	s__Sphingomonas trueperi	80.4427	618	1458	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	80.4396	660	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	80.3535	671	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091475.1	s__Sphingomonas azotifigens	80.3519	622	1458	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	80.3106	662	1458	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	80.2778	605	1458	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	80.1928	558	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014489075.1	s__Sphingomonas sp014489075	80.1522	644	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591025.1	s__Sphingomonas soli	79.8377	506	1458	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833215.1	s__Sphingomonas sp007833215	79.0418	463	1458	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 13:22:44,942] [INFO] GTDB search result was written to GCF_014199255.1_ASM1419925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:44,943] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:44,946] [INFO] DFAST_QC result json was written to GCF_014199255.1_ASM1419925v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:44,947] [INFO] DFAST_QC completed!
[2024-01-24 13:22:44,947] [INFO] Total running time: 0h1m34s