[2024-01-24 13:16:56,309] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,311] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference
[2024-01-24 13:16:57,553] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,553] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,554] [INFO] Running command: gunzip -c /var/lib/cwl/stg49d8c5fe-60ef-4fc3-9e5a-e7f96e019ae3/GCF_001591045.1_ASM159104v1_genomic.fna.gz | prodigal -d GCF_001591045.1_ASM159104v1_genomic.fna/cds.fna -a GCF_001591045.1_ASM159104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:08,392] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:08,393] [INFO] Task started: HMMsearch
[2024-01-24 13:17:08,393] [INFO] Running command: hmmsearch --tblout GCF_001591045.1_ASM159104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/reference_markers.hmm GCF_001591045.1_ASM159104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:08,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:08,689] [INFO] Found 6/6 markers.
[2024-01-24 13:17:08,724] [INFO] Query marker FASTA was written to GCF_001591045.1_ASM159104v1_genomic.fna/markers.fasta
[2024-01-24 13:17:08,724] [INFO] Task started: Blastn
[2024-01-24 13:17:08,724] [INFO] Running command: blastn -query GCF_001591045.1_ASM159104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/reference_markers.fasta -out GCF_001591045.1_ASM159104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:09,714] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:09,719] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:09,720] [INFO] Target genome list was writen to GCF_001591045.1_ASM159104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:09,727] [INFO] Task started: fastANI
[2024-01-24 13:17:09,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d8c5fe-60ef-4fc3-9e5a-e7f96e019ae3/GCF_001591045.1_ASM159104v1_genomic.fna.gz --refList GCF_001591045.1_ASM159104v1_genomic.fna/target_genomes.txt --output GCF_001591045.1_ASM159104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:23,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:23,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:23,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:23,153] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:23,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:23,153] [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 granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	100.0	1324	1330	95	conclusive
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	86.2466	835	1330	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	85.19	743	1330	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	85.0034	778	1330	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	84.3652	755	1330	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.2983	694	1330	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	84.1491	778	1330	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	84.138	818	1330	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	84.0818	767	1330	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	84.0345	781	1330	95	below_threshold
Sphingopyxis flava	strain=R11H	GCA_900168005.1	1507287	1507287	type	True	82.3145	703	1330	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.7324	413	1330	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.4372	391	1330	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.3393	370	1330	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.97	463	1330	95	below_threshold
Sphingomonas piscis	strain=HDW15B	GCA_011300455.1	2714943	2714943	type	True	77.7471	189	1330	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:23,155] [INFO] DFAST Taxonomy check result was written to GCF_001591045.1_ASM159104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:23,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:23,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:23,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/checkm_data
[2024-01-24 13:17:23,157] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:23,197] [INFO] Task started: CheckM
[2024-01-24 13:17:23,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591045.1_ASM159104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591045.1_ASM159104v1_genomic.fna/checkm_input GCF_001591045.1_ASM159104v1_genomic.fna/checkm_result
[2024-01-24 13:17:58,927] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:58,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:58,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:58,955] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:58,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591045.1_ASM159104v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:58,956] [INFO] Task started: Blastn
[2024-01-24 13:17:58,956] [INFO] Running command: blastn -query GCF_001591045.1_ASM159104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1d7e3a0-9413-4d89-bbb7-1769a4e72e06/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591045.1_ASM159104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:00,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:00,886] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:00,886] [INFO] Target genome list was writen to GCF_001591045.1_ASM159104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:00,895] [INFO] Task started: fastANI
[2024-01-24 13:18:00,895] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d8c5fe-60ef-4fc3-9e5a-e7f96e019ae3/GCF_001591045.1_ASM159104v1_genomic.fna.gz --refList GCF_001591045.1_ASM159104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591045.1_ASM159104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:11,756] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:11,771] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:11,771] [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_001591045.1	s__Sphingopyxis granuli	100.0	1324	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	conclusive
GCF_014199295.1	s__Sphingopyxis panaciterrulae	86.2718	831	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002277025.1	s__Sphingopyxis sp002277025	86.0502	818	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188185.1	s__Sphingopyxis indica	85.1898	743	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842935.1	s__Sphingopyxis sp002842935	84.9769	540	1330	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	84.8108	799	1330	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	84.2668	696	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307295.1	s__Sphingopyxis macrogoltabida_B	84.233	781	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468395.1	s__Sphingopyxis sp001468395	84.2113	735	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	84.1618	816	1330	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001278035.1	s__Sphingopyxis sp001278035	82.3534	727	1330	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 13:18:11,773] [INFO] GTDB search result was written to GCF_001591045.1_ASM159104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:11,773] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:11,777] [INFO] DFAST_QC result json was written to GCF_001591045.1_ASM159104v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:11,777] [INFO] DFAST_QC completed!
[2024-01-24 13:18:11,777] [INFO] Total running time: 0h1m15s