[2024-01-25 19:37:05,616] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:05,618] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:05,618] [INFO] DQC Reference Directory: /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference
[2024-01-25 19:37:06,759] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:06,764] [INFO] Task started: Prodigal
[2024-01-25 19:37:06,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d8fabb6-b718-4637-8397-e0151076247b/GCF_000974765.1_ASM97476v1_genomic.fna.gz | prodigal -d GCF_000974765.1_ASM97476v1_genomic.fna/cds.fna -a GCF_000974765.1_ASM97476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:14,577] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:14,577] [INFO] Task started: HMMsearch
[2024-01-25 19:37:14,578] [INFO] Running command: hmmsearch --tblout GCF_000974765.1_ASM97476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/reference_markers.hmm GCF_000974765.1_ASM97476v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:14,808] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:14,809] [INFO] Found 6/6 markers.
[2024-01-25 19:37:14,836] [INFO] Query marker FASTA was written to GCF_000974765.1_ASM97476v1_genomic.fna/markers.fasta
[2024-01-25 19:37:14,836] [INFO] Task started: Blastn
[2024-01-25 19:37:14,836] [INFO] Running command: blastn -query GCF_000974765.1_ASM97476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/reference_markers.fasta -out GCF_000974765.1_ASM97476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:15,744] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:15,747] [INFO] Selected 20 target genomes.
[2024-01-25 19:37:15,747] [INFO] Target genome list was writen to GCF_000974765.1_ASM97476v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:15,752] [INFO] Task started: fastANI
[2024-01-25 19:37:15,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d8fabb6-b718-4637-8397-e0151076247b/GCF_000974765.1_ASM97476v1_genomic.fna.gz --refList GCF_000974765.1_ASM97476v1_genomic.fna/target_genomes.txt --output GCF_000974765.1_ASM97476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:31,688] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:31,688] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:31,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:31,701] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:31,702] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:31,702] [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 changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	100.0	1043	1043	95	conclusive
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	86.0934	815	1043	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	80.1706	491	1043	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.4289	427	1043	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.2262	442	1043	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.2246	446	1043	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	79.2177	446	1043	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	78.9412	368	1043	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.8768	371	1043	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.8346	363	1043	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	78.7983	435	1043	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	78.7805	370	1043	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.7562	377	1043	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.738	362	1043	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.7039	373	1043	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.6841	375	1043	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.6602	390	1043	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	78.6577	387	1043	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	78.6022	391	1043	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	78.1165	275	1043	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:31,703] [INFO] DFAST Taxonomy check result was written to GCF_000974765.1_ASM97476v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:31,705] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:31,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:31,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/checkm_data
[2024-01-25 19:37:31,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:31,739] [INFO] Task started: CheckM
[2024-01-25 19:37:31,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000974765.1_ASM97476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000974765.1_ASM97476v1_genomic.fna/checkm_input GCF_000974765.1_ASM97476v1_genomic.fna/checkm_result
[2024-01-25 19:37:57,496] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:57,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:57,517] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:57,517] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:57,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000974765.1_ASM97476v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:57,518] [INFO] Task started: Blastn
[2024-01-25 19:37:57,518] [INFO] Running command: blastn -query GCF_000974765.1_ASM97476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged626403-ec0b-4540-bb7a-2e4d0bdc89b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000974765.1_ASM97476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:59,294] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:59,297] [INFO] Selected 11 target genomes.
[2024-01-25 19:37:59,297] [INFO] Target genome list was writen to GCF_000974765.1_ASM97476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:59,305] [INFO] Task started: fastANI
[2024-01-25 19:37:59,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d8fabb6-b718-4637-8397-e0151076247b/GCF_000974765.1_ASM97476v1_genomic.fna.gz --refList GCF_000974765.1_ASM97476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000974765.1_ASM97476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:08,100] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:08,108] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:08,108] [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_000974765.1	s__Sphingomonas_B changbaiensis	100.0	1043	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009753715.1	s__Sphingomonas_B horti	86.0586	818	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	82.1809	629	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044515.1	s__Sphingomonas_B sp013044515	81.8734	630	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	80.1824	490	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	79.9792	356	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	78.7698	438	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	78.695	414	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	78.6691	427	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	78.6401	374	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	78.1202	274	1043	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:08,110] [INFO] GTDB search result was written to GCF_000974765.1_ASM97476v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:08,110] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:08,114] [INFO] DFAST_QC result json was written to GCF_000974765.1_ASM97476v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:08,114] [INFO] DFAST_QC completed!
[2024-01-25 19:38:08,114] [INFO] Total running time: 0h1m2s