[2024-01-24 13:19:13,082] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:13,083] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:13,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference
[2024-01-24 13:19:14,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:14,367] [INFO] Task started: Prodigal
[2024-01-24 13:19:14,368] [INFO] Running command: gunzip -c /var/lib/cwl/stge36241d0-d737-4f21-b2b8-e0549988bdb2/GCF_007859635.1_ASM785963v1_genomic.fna.gz | prodigal -d GCF_007859635.1_ASM785963v1_genomic.fna/cds.fna -a GCF_007859635.1_ASM785963v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:24,357] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:24,357] [INFO] Task started: HMMsearch
[2024-01-24 13:19:24,357] [INFO] Running command: hmmsearch --tblout GCF_007859635.1_ASM785963v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/reference_markers.hmm GCF_007859635.1_ASM785963v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:24,619] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:24,620] [INFO] Found 6/6 markers.
[2024-01-24 13:19:24,652] [INFO] Query marker FASTA was written to GCF_007859635.1_ASM785963v1_genomic.fna/markers.fasta
[2024-01-24 13:19:24,653] [INFO] Task started: Blastn
[2024-01-24 13:19:24,653] [INFO] Running command: blastn -query GCF_007859635.1_ASM785963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/reference_markers.fasta -out GCF_007859635.1_ASM785963v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:25,601] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:25,605] [INFO] Selected 22 target genomes.
[2024-01-24 13:19:25,606] [INFO] Target genome list was writen to GCF_007859635.1_ASM785963v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:25,625] [INFO] Task started: fastANI
[2024-01-24 13:19:25,625] [INFO] Running command: fastANI --query /var/lib/cwl/stge36241d0-d737-4f21-b2b8-e0549988bdb2/GCF_007859635.1_ASM785963v1_genomic.fna.gz --refList GCF_007859635.1_ASM785963v1_genomic.fna/target_genomes.txt --output GCF_007859635.1_ASM785963v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:42,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:42,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:42,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:42,804] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:42,804] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:42,804] [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 panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	100.0	1134	1134	95	conclusive
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	82.0762	709	1134	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	82.0	746	1134	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	81.9112	701	1134	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.0118	556	1134	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	79.8802	532	1134	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.8406	566	1134	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	79.5925	446	1134	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	79.5678	492	1134	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	79.4887	528	1134	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.4798	471	1134	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	79.4391	499	1134	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.3528	485	1134	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.3417	497	1134	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	79.33	507	1134	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.2761	473	1134	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.1971	486	1134	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.1571	494	1134	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.0514	500	1134	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.0362	479	1134	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.9422	496	1134	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	78.9137	484	1134	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,806] [INFO] DFAST Taxonomy check result was written to GCF_007859635.1_ASM785963v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:42,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:42,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:42,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/checkm_data
[2024-01-24 13:19:42,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:42,843] [INFO] Task started: CheckM
[2024-01-24 13:19:42,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859635.1_ASM785963v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859635.1_ASM785963v1_genomic.fna/checkm_input GCF_007859635.1_ASM785963v1_genomic.fna/checkm_result
[2024-01-24 13:20:14,744] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:14,746] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:14,767] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:14,767] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:14,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859635.1_ASM785963v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:14,768] [INFO] Task started: Blastn
[2024-01-24 13:20:14,768] [INFO] Running command: blastn -query GCF_007859635.1_ASM785963v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a92cb2d-85e6-4d91-9a7b-aada19e67c92/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859635.1_ASM785963v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:16,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:16,582] [INFO] Selected 14 target genomes.
[2024-01-24 13:20:16,582] [INFO] Target genome list was writen to GCF_007859635.1_ASM785963v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:16,600] [INFO] Task started: fastANI
[2024-01-24 13:20:16,600] [INFO] Running command: fastANI --query /var/lib/cwl/stge36241d0-d737-4f21-b2b8-e0549988bdb2/GCF_007859635.1_ASM785963v1_genomic.fna.gz --refList GCF_007859635.1_ASM785963v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859635.1_ASM785963v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:28,201] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:28,218] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:28,218] [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_007859635.1	s__Sphingomonas panacisoli	100.0	1134	1134	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_017304615.1	s__Sphingomonas sp017304615	85.6443	770	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799495.1	s__Sphingomonas sp004799495	84.8524	781	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	83.3761	718	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598455.1	s__Sphingomonas pruni	82.0469	711	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598415.1	s__Sphingomonas mali	82.0233	743	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598355.1	s__Sphingomonas asaccharolytica	81.9123	700	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	79.8892	531	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	79.5268	547	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_003550065.1	s__Sphingomonas caeni	79.4502	529	1134	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	79.4154	511	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556185.1	s__Sphingomonas sp001556185	79.3924	487	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.51	96.51	0.87	0.87	2	-
GCF_002002925.1	s__Sphingomonas sp002002925	79.3732	524	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	79.211	427	1134	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:28,220] [INFO] GTDB search result was written to GCF_007859635.1_ASM785963v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:28,220] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:28,225] [INFO] DFAST_QC result json was written to GCF_007859635.1_ASM785963v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:28,225] [INFO] DFAST_QC completed!
[2024-01-24 13:20:28,225] [INFO] Total running time: 0h1m15s