[2024-01-24 13:40:44,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference
[2024-01-24 13:40:45,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,438] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,439] [INFO] Running command: gunzip -c /var/lib/cwl/stgb0f5093b-7121-4930-b00d-09dfab2dd24b/GCF_000013985.1_ASM1398v1_genomic.fna.gz | prodigal -d GCF_000013985.1_ASM1398v1_genomic.fna/cds.fna -a GCF_000013985.1_ASM1398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:56,157] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:56,157] [INFO] Task started: HMMsearch
[2024-01-24 13:40:56,158] [INFO] Running command: hmmsearch --tblout GCF_000013985.1_ASM1398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/reference_markers.hmm GCF_000013985.1_ASM1398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:56,474] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:56,475] [INFO] Found 6/6 markers.
[2024-01-24 13:40:56,506] [INFO] Query marker FASTA was written to GCF_000013985.1_ASM1398v1_genomic.fna/markers.fasta
[2024-01-24 13:40:56,506] [INFO] Task started: Blastn
[2024-01-24 13:40:56,506] [INFO] Running command: blastn -query GCF_000013985.1_ASM1398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/reference_markers.fasta -out GCF_000013985.1_ASM1398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,452] [INFO] Selected 19 target genomes.
[2024-01-24 13:40:57,452] [INFO] Target genome list was writen to GCF_000013985.1_ASM1398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:57,458] [INFO] Task started: fastANI
[2024-01-24 13:40:57,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0f5093b-7121-4930-b00d-09dfab2dd24b/GCF_000013985.1_ASM1398v1_genomic.fna.gz --refList GCF_000013985.1_ASM1398v1_genomic.fna/target_genomes.txt --output GCF_000013985.1_ASM1398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,399] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:15,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,399] [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 alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	100.0	1124	1124	95	conclusive
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	86.0087	843	1124	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	85.0571	758	1124	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	85.0326	831	1124	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.7531	784	1124	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	84.5378	781	1124	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.4978	823	1124	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.3515	766	1124	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	84.0983	803	1124	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	84.0539	769	1124	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	83.8807	763	1124	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	83.7893	734	1124	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	83.7391	741	1124	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	83.5985	776	1124	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2807	380	1124	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.7725	355	1124	95	below_threshold
Novosphingobium aquimarinum	strain=M24A2M	GCA_009746585.1	2682494	2682494	type	True	77.6637	258	1124	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.5782	364	1124	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.4788	191	1124	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,401] [INFO] DFAST Taxonomy check result was written to GCF_000013985.1_ASM1398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/checkm_data
[2024-01-24 13:41:15,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:15,440] [INFO] Task started: CheckM
[2024-01-24 13:41:15,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000013985.1_ASM1398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000013985.1_ASM1398v1_genomic.fna/checkm_input GCF_000013985.1_ASM1398v1_genomic.fna/checkm_result
[2024-01-24 13:41:51,067] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:51,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:51,089] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:51,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:51,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000013985.1_ASM1398v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:51,090] [INFO] Task started: Blastn
[2024-01-24 13:41:51,091] [INFO] Running command: blastn -query GCF_000013985.1_ASM1398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1658be5d-9ca2-4131-bd4f-9b766dfdaa48/dqc_reference/reference_markers_gtdb.fasta -out GCF_000013985.1_ASM1398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,801] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,805] [INFO] Selected 14 target genomes.
[2024-01-24 13:41:52,805] [INFO] Target genome list was writen to GCF_000013985.1_ASM1398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:52,825] [INFO] Task started: fastANI
[2024-01-24 13:41:52,826] [INFO] Running command: fastANI --query /var/lib/cwl/stgb0f5093b-7121-4930-b00d-09dfab2dd24b/GCF_000013985.1_ASM1398v1_genomic.fna.gz --refList GCF_000013985.1_ASM1398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000013985.1_ASM1398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:06,676] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,695] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:06,695] [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_000013985.1	s__Sphingopyxis alaskensis	100.0	1124	1124	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_003609835.1	s__Sphingopyxis sp003609835	90.0608	916	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595975.1	s__Sphingopyxis sp014595975	89.2995	859	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	86.3785	833	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756385.1	s__Sphingopyxis sp000756385	86.3588	825	1124	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	86.0245	842	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	85.8643	851	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	85.7956	829	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
GCF_001468465.1	s__Sphingopyxis sp001468465	85.4053	821	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015475875.1	s__Sphingopyxis solisilvae	85.0592	757	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.45	96.45	0.86	0.86	2	-
GCF_001468395.1	s__Sphingopyxis sp001468395	84.9504	839	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCA_017309275.1	s__Sphingopyxis sp017309275	84.4121	803	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	84.3576	764	1124	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793775.1	s__Sphingopyxis sp016793775	84.0854	764	1124	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 13:42:06,697] [INFO] GTDB search result was written to GCF_000013985.1_ASM1398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:06,698] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:06,701] [INFO] DFAST_QC result json was written to GCF_000013985.1_ASM1398v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:06,702] [INFO] DFAST_QC completed!
[2024-01-24 13:42:06,702] [INFO] Total running time: 0h1m23s