[2024-01-24 13:35:27,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,346] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,347] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference
[2024-01-24 13:35:28,559] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,560] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,560] [INFO] Running command: gunzip -c /var/lib/cwl/stg28128ebb-e546-4827-8930-f6b2c08a08ab/GCF_002205635.1_ASM220563v1_genomic.fna.gz | prodigal -d GCF_002205635.1_ASM220563v1_genomic.fna/cds.fna -a GCF_002205635.1_ASM220563v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:41,095] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:41,095] [INFO] Task started: HMMsearch
[2024-01-24 13:35:41,096] [INFO] Running command: hmmsearch --tblout GCF_002205635.1_ASM220563v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/reference_markers.hmm GCF_002205635.1_ASM220563v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:41,380] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:41,382] [INFO] Found 6/6 markers.
[2024-01-24 13:35:41,421] [INFO] Query marker FASTA was written to GCF_002205635.1_ASM220563v1_genomic.fna/markers.fasta
[2024-01-24 13:35:41,422] [INFO] Task started: Blastn
[2024-01-24 13:35:41,422] [INFO] Running command: blastn -query GCF_002205635.1_ASM220563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/reference_markers.fasta -out GCF_002205635.1_ASM220563v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:42,340] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:42,344] [INFO] Selected 16 target genomes.
[2024-01-24 13:35:42,344] [INFO] Target genome list was writen to GCF_002205635.1_ASM220563v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:42,361] [INFO] Task started: fastANI
[2024-01-24 13:35:42,361] [INFO] Running command: fastANI --query /var/lib/cwl/stg28128ebb-e546-4827-8930-f6b2c08a08ab/GCF_002205635.1_ASM220563v1_genomic.fna.gz --refList GCF_002205635.1_ASM220563v1_genomic.fna/target_genomes.txt --output GCF_002205635.1_ASM220563v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:56,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:56,807] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:56,807] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:56,826] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:35:56,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:56,826] [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
Sphingopyxis witflariensis	strain=DSM 14551	GCA_002205635.1	173675	173675	type	True	100.0	1413	1417	95	conclusive
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	84.3459	879	1417	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.2807	840	1417	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.2031	854	1417	95	below_threshold
Sphingopyxis microcysteis	strain=Z10-6	GCA_012274265.1	2484145	2484145	type	True	84.0407	805	1417	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	83.9655	895	1417	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	83.7295	748	1417	95	below_threshold
Sphingopyxis bauzanensis	strain=CGMCC 1.8959	GCA_014645635.1	651663	651663	type	True	83.7232	798	1417	95	below_threshold
Sphingopyxis bauzanensis	strain=DSM 22271	GCA_002205675.1	651663	651663	type	True	83.7173	806	1417	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	83.145	791	1417	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	82.8804	746	1417	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.2398	369	1417	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.768	337	1417	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.6898	335	1417	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.6663	320	1417	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.4668	218	1417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:56,828] [INFO] DFAST Taxonomy check result was written to GCF_002205635.1_ASM220563v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:56,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:56,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:56,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/checkm_data
[2024-01-24 13:35:56,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:56,875] [INFO] Task started: CheckM
[2024-01-24 13:35:56,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002205635.1_ASM220563v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002205635.1_ASM220563v1_genomic.fna/checkm_input GCF_002205635.1_ASM220563v1_genomic.fna/checkm_result
[2024-01-24 13:36:35,413] [INFO] Task succeeded: CheckM
[2024-01-24 13:36:35,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:36:35,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:36:35,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:36:35,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002205635.1_ASM220563v1_genomic.fna/markers.fasta)
[2024-01-24 13:36:35,437] [INFO] Task started: Blastn
[2024-01-24 13:36:35,438] [INFO] Running command: blastn -query GCF_002205635.1_ASM220563v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9745b9e-f3c3-493b-b6c9-47ee83ae96db/dqc_reference/reference_markers_gtdb.fasta -out GCF_002205635.1_ASM220563v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:37,250] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:37,255] [INFO] Selected 20 target genomes.
[2024-01-24 13:36:37,255] [INFO] Target genome list was writen to GCF_002205635.1_ASM220563v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:36:37,293] [INFO] Task started: fastANI
[2024-01-24 13:36:37,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg28128ebb-e546-4827-8930-f6b2c08a08ab/GCF_002205635.1_ASM220563v1_genomic.fna.gz --refList GCF_002205635.1_ASM220563v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002205635.1_ASM220563v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:56,814] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:56,844] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:56,844] [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_002205635.1	s__Sphingopyxis witflariensis	100.0	1413	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001468225.1	s__Sphingopyxis sp001468225	85.1577	940	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.97	0.98	0.96	8	-
GCF_000756375.1	s__Sphingopyxis sp000756375	84.7452	896	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427105.1	s__Sphingopyxis sp001427105	84.6823	896	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005503215.1	s__Sphingopyxis sp005503215	84.6204	902	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.20	99.20	0.88	0.88	2	-
GCF_000803645.1	s__Sphingopyxis fribergensis	84.336	881	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	84.3177	886	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011926545.1	s__Sphingopyxis italica	84.2666	841	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503695.1	s__Sphingopyxis sp003609815	84.2485	831	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.15	97.15	0.90	0.90	2	-
GCF_011762125.1	s__Sphingopyxis panaciterrae	84.2146	853	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821905.1	s__Sphingopyxis sp013821905	84.174	652	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797775.2	s__Sphingopyxis sp001427085	84.1654	862	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.11	97.01	0.89	0.87	3	-
GCF_013410105.1	s__Sphingopyxis sp013410105	84.0052	849	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	83.9443	898	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCA_018823905.1	s__Sphingopyxis sp018823905	83.7879	733	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	-
GCA_002454115.1	s__Sphingopyxis sp002454115	83.7344	779	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCF_001047015.1	s__Sphingopyxis sp001047015	83.5675	870	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	83.4992	750	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	83.058	819	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657575.1	s__Sphingopyxis sp015657575	82.7344	570	1417	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:56,846] [INFO] GTDB search result was written to GCF_002205635.1_ASM220563v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:56,846] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:56,850] [INFO] DFAST_QC result json was written to GCF_002205635.1_ASM220563v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:56,851] [INFO] DFAST_QC completed!
[2024-01-24 13:36:56,851] [INFO] Total running time: 0h1m30s