[2024-01-24 15:02:07,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,443] [INFO] DQC Reference Directory: /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference
[2024-01-24 15:02:09,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,604] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,604] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9613132-9203-4e94-a19e-c11c7f4ea6de/GCF_027922045.1_ASM2792204v1_genomic.fna.gz | prodigal -d GCF_027922045.1_ASM2792204v1_genomic.fna/cds.fna -a GCF_027922045.1_ASM2792204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:20,571] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:20,571] [INFO] Task started: HMMsearch
[2024-01-24 15:02:20,571] [INFO] Running command: hmmsearch --tblout GCF_027922045.1_ASM2792204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/reference_markers.hmm GCF_027922045.1_ASM2792204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:20,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:20,858] [INFO] Found 6/6 markers.
[2024-01-24 15:02:20,897] [INFO] Query marker FASTA was written to GCF_027922045.1_ASM2792204v1_genomic.fna/markers.fasta
[2024-01-24 15:02:20,897] [INFO] Task started: Blastn
[2024-01-24 15:02:20,897] [INFO] Running command: blastn -query GCF_027922045.1_ASM2792204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/reference_markers.fasta -out GCF_027922045.1_ASM2792204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:21,884] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:21,887] [INFO] Selected 22 target genomes.
[2024-01-24 15:02:21,887] [INFO] Target genome list was writen to GCF_027922045.1_ASM2792204v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:21,926] [INFO] Task started: fastANI
[2024-01-24 15:02:21,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9613132-9203-4e94-a19e-c11c7f4ea6de/GCF_027922045.1_ASM2792204v1_genomic.fna.gz --refList GCF_027922045.1_ASM2792204v1_genomic.fna/target_genomes.txt --output GCF_027922045.1_ASM2792204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:39,807] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:39,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:39,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:39,826] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:39,826] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:39,826] [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
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	91.8607	965	1234	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	91.8372	958	1234	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	81.8028	568	1234	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	80.9496	522	1234	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	80.1339	571	1234	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	80.08	498	1234	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	80.0511	498	1234	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.048	571	1234	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.017	584	1234	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.0024	546	1234	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	79.9684	562	1234	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	79.8542	559	1234	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	79.7973	536	1234	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.7795	541	1234	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	79.6772	438	1234	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.5998	484	1234	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.4971	590	1234	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.4212	476	1234	95	below_threshold
Sphingomonas japonica	strain=DSM 22753	GCA_011762085.1	511662	511662	type	True	79.4133	465	1234	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.2398	459	1234	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	79.1087	477	1234	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	78.8797	429	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:39,828] [INFO] DFAST Taxonomy check result was written to GCF_027922045.1_ASM2792204v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:39,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:39,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:39,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/checkm_data
[2024-01-24 15:02:39,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:39,868] [INFO] Task started: CheckM
[2024-01-24 15:02:39,868] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027922045.1_ASM2792204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027922045.1_ASM2792204v1_genomic.fna/checkm_input GCF_027922045.1_ASM2792204v1_genomic.fna/checkm_result
[2024-01-24 15:03:17,108] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:17,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:17,128] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:17,129] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:17,129] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027922045.1_ASM2792204v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:17,130] [INFO] Task started: Blastn
[2024-01-24 15:03:17,130] [INFO] Running command: blastn -query GCF_027922045.1_ASM2792204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge592afff-a89a-4d4f-95ef-10bad630739b/dqc_reference/reference_markers_gtdb.fasta -out GCF_027922045.1_ASM2792204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:19,141] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:19,145] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:19,145] [INFO] Target genome list was writen to GCF_027922045.1_ASM2792204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:19,169] [INFO] Task started: fastANI
[2024-01-24 15:03:19,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9613132-9203-4e94-a19e-c11c7f4ea6de/GCF_027922045.1_ASM2792204v1_genomic.fna.gz --refList GCF_027922045.1_ASM2792204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027922045.1_ASM2792204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:36,328] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:36,344] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:36,344] [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_004341505.2	s__Sphingomonas sp004341505	95.3431	1033	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	conclusive
GCF_004135605.1	s__Sphingomonas desiccabilis	91.8607	965	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018449795.1	s__Sphingomonas sp018449795	80.2382	520	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001619955.1	s__Sphingomonas hankookensis	80.0783	548	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.49	99.35	0.90	0.87	3	-
GCA_003240755.1	s__Sphingomonas hengshuiensis_A	80.0484	499	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425385.1	s__Sphingomonas sp001425385	79.9986	569	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.44	96.89	0.96	0.93	3	-
GCF_001421765.1	s__Sphingomonas sp001421765	79.9883	548	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000632225.1	s__Sphingomonas sp000632225	79.9592	547	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	79.9535	587	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.8978	550	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.773	606	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	79.7269	447	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCF_001421715.1	s__Sphingomonas sp001421715	79.6945	533	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.52	97.51	0.91	0.91	3	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.5508	478	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_012927115.1	s__Sphingomonas sp012927115	79.5187	477	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	79.4918	466	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	79.3728	483	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842075.1	s__Sphingomonas sp014842075	79.1049	495	1234	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 15:03:36,346] [INFO] GTDB search result was written to GCF_027922045.1_ASM2792204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:36,346] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:36,351] [INFO] DFAST_QC result json was written to GCF_027922045.1_ASM2792204v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:36,352] [INFO] DFAST_QC completed!
[2024-01-24 15:03:36,352] [INFO] Total running time: 0h1m29s