[2024-01-24 11:05:26,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:26,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:26,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference
[2024-01-24 11:05:27,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:27,795] [INFO] Task started: Prodigal
[2024-01-24 11:05:27,796] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d73afa2-97f0-4ecd-b7fe-d9440cbdfce4/GCF_019204005.1_ASM1920400v1_genomic.fna.gz | prodigal -d GCF_019204005.1_ASM1920400v1_genomic.fna/cds.fna -a GCF_019204005.1_ASM1920400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:37,530] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:37,531] [INFO] Task started: HMMsearch
[2024-01-24 11:05:37,531] [INFO] Running command: hmmsearch --tblout GCF_019204005.1_ASM1920400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/reference_markers.hmm GCF_019204005.1_ASM1920400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:37,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:37,788] [INFO] Found 6/6 markers.
[2024-01-24 11:05:37,815] [INFO] Query marker FASTA was written to GCF_019204005.1_ASM1920400v1_genomic.fna/markers.fasta
[2024-01-24 11:05:37,815] [INFO] Task started: Blastn
[2024-01-24 11:05:37,815] [INFO] Running command: blastn -query GCF_019204005.1_ASM1920400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/reference_markers.fasta -out GCF_019204005.1_ASM1920400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:38,668] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:38,679] [INFO] Selected 27 target genomes.
[2024-01-24 11:05:38,679] [INFO] Target genome list was writen to GCF_019204005.1_ASM1920400v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:38,693] [INFO] Task started: fastANI
[2024-01-24 11:05:38,693] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d73afa2-97f0-4ecd-b7fe-d9440cbdfce4/GCF_019204005.1_ASM1920400v1_genomic.fna.gz --refList GCF_019204005.1_ASM1920400v1_genomic.fna/target_genomes.txt --output GCF_019204005.1_ASM1920400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:55,623] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:55,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:55,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:55,644] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:55,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:55,644] [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
Pacificimonas flava	strain=JLT2015	GCA_000342165.1	1234595	1234595	type	True	77.5682	264	1003	95	below_threshold
Pacificimonas flava	strain=DSM 107612	GCA_014202205.1	1234595	1234595	type	True	77.5642	266	1003	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.0258	138	1003	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	76.9328	134	1003	95	below_threshold
Sphingosinicella soli	strain=DSM 17328	GCA_014199685.1	333708	333708	type	True	76.9195	164	1003	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.9147	143	1003	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	76.9112	118	1003	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	76.8787	89	1003	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	76.813	78	1003	95	below_threshold
Sphingosinicella microcystinivorans	strain=DSM 19791	GCA_003634215.1	335406	335406	type	True	76.7886	163	1003	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.7773	127	1003	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	76.7584	115	1003	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.7538	134	1003	95	below_threshold
Tardibacter chloracetimidivorans	strain=JJ-A5	GCA_001890385.1	1921510	1921510	type	True	76.7309	96	1003	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	76.6386	131	1003	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	76.6011	141	1003	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	76.533	138	1003	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	76.4758	148	1003	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	76.4459	124	1003	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.428	124	1003	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	76.409	144	1003	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	76.4065	114	1003	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	76.396	133	1003	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	76.285	104	1003	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	76.1997	155	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:55,646] [INFO] DFAST Taxonomy check result was written to GCF_019204005.1_ASM1920400v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:55,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:55,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:55,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/checkm_data
[2024-01-24 11:05:55,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:55,682] [INFO] Task started: CheckM
[2024-01-24 11:05:55,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019204005.1_ASM1920400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019204005.1_ASM1920400v1_genomic.fna/checkm_input GCF_019204005.1_ASM1920400v1_genomic.fna/checkm_result
[2024-01-24 11:06:28,002] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:28,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:28,025] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:28,025] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:28,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019204005.1_ASM1920400v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:28,026] [INFO] Task started: Blastn
[2024-01-24 11:06:28,026] [INFO] Running command: blastn -query GCF_019204005.1_ASM1920400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58a1af9a-461a-4b0e-b4c2-fb066f02ac5d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019204005.1_ASM1920400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:29,617] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:29,621] [INFO] Selected 17 target genomes.
[2024-01-24 11:06:29,621] [INFO] Target genome list was writen to GCF_019204005.1_ASM1920400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:29,636] [INFO] Task started: fastANI
[2024-01-24 11:06:29,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d73afa2-97f0-4ecd-b7fe-d9440cbdfce4/GCF_019204005.1_ASM1920400v1_genomic.fna.gz --refList GCF_019204005.1_ASM1920400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019204005.1_ASM1920400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:41,360] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:41,384] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:41,384] [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
GCA_019204005.1	s__Pacificimonas sp019204005	100.0	1002	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002375465.1	s__Pacificimonas sp002375465	78.3076	334	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342165.1	s__Pacificimonas flava	77.5804	263	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002211145.1	s__Pacificimonas flava_A	77.3713	242	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pacificimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	76.847	131	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634215.1	s__Sphingosinicella microcystinivorans	76.7886	163	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000016765.1	s__Rhizorhabdus wittichii	76.7286	156	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_014199325.1	s__Sphingomonas yantingensis	76.6011	141	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.75	96.75	0.89	0.89	2	-
GCA_016793845.1	s__Sphingosinicella sp016793845	76.5567	127	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468395.1	s__Sphingopyxis sp001468395	76.5516	137	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCA_900078365.1	s__Sphingopyxis sp900078365	76.5326	123	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	76.5003	129	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	76.4802	152	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	76.4642	149	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_903643035.1	s__Sphingomonas sp903643035	76.0086	77	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423025.1	s__Polymorphobacter sp002423025	75.7169	77	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Polymorphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873545.1	s__OAS926 sp014873545	75.6296	79	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__OAS926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:41,386] [INFO] GTDB search result was written to GCF_019204005.1_ASM1920400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:41,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:41,393] [INFO] DFAST_QC result json was written to GCF_019204005.1_ASM1920400v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:41,393] [INFO] DFAST_QC completed!
[2024-01-24 11:06:41,393] [INFO] Total running time: 0h1m15s