[2024-01-24 13:36:28,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:28,102] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:28,103] [INFO] DQC Reference Directory: /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference
[2024-01-24 13:36:29,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:29,325] [INFO] Task started: Prodigal
[2024-01-24 13:36:29,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg955e14f6-9d16-4902-9605-52409afa899c/GCF_000264945.2_ASM26494v2_genomic.fna.gz | prodigal -d GCF_000264945.2_ASM26494v2_genomic.fna/cds.fna -a GCF_000264945.2_ASM26494v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:40,974] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:40,975] [INFO] Task started: HMMsearch
[2024-01-24 13:36:40,975] [INFO] Running command: hmmsearch --tblout GCF_000264945.2_ASM26494v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/reference_markers.hmm GCF_000264945.2_ASM26494v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:41,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:41,255] [INFO] Found 6/6 markers.
[2024-01-24 13:36:41,290] [INFO] Query marker FASTA was written to GCF_000264945.2_ASM26494v2_genomic.fna/markers.fasta
[2024-01-24 13:36:41,290] [INFO] Task started: Blastn
[2024-01-24 13:36:41,291] [INFO] Running command: blastn -query GCF_000264945.2_ASM26494v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/reference_markers.fasta -out GCF_000264945.2_ASM26494v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:42,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:42,235] [INFO] Selected 12 target genomes.
[2024-01-24 13:36:42,235] [INFO] Target genome list was writen to GCF_000264945.2_ASM26494v2_genomic.fna/target_genomes.txt
[2024-01-24 13:36:42,241] [INFO] Task started: fastANI
[2024-01-24 13:36:42,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg955e14f6-9d16-4902-9605-52409afa899c/GCF_000264945.2_ASM26494v2_genomic.fna.gz --refList GCF_000264945.2_ASM26494v2_genomic.fna/target_genomes.txt --output GCF_000264945.2_ASM26494v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:53,875] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:53,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:53,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:53,887] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:53,887] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:53,887] [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
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	100.0	1313	1314	95	conclusive
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	91.6962	957	1314	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	91.6879	961	1314	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	89.5618	851	1314	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_001598515.1	46429	46429	type	True	89.5017	788	1314	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	87.5178	865	1314	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	86.4789	777	1314	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.1619	702	1314	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.7276	382	1314	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.4753	360	1314	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.3345	395	1314	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.3242	376	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:53,889] [INFO] DFAST Taxonomy check result was written to GCF_000264945.2_ASM26494v2_genomic.fna/tc_result.tsv
[2024-01-24 13:36:53,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:53,890] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:53,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/checkm_data
[2024-01-24 13:36:53,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:53,934] [INFO] Task started: CheckM
[2024-01-24 13:36:53,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000264945.2_ASM26494v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000264945.2_ASM26494v2_genomic.fna/checkm_input GCF_000264945.2_ASM26494v2_genomic.fna/checkm_result
[2024-01-24 13:37:32,081] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:32,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:32,102] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:32,103] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:32,103] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000264945.2_ASM26494v2_genomic.fna/markers.fasta)
[2024-01-24 13:37:32,104] [INFO] Task started: Blastn
[2024-01-24 13:37:32,104] [INFO] Running command: blastn -query GCF_000264945.2_ASM26494v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1beb7eca-d7ca-4a52-a5a4-72b97c87591a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000264945.2_ASM26494v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,138] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,141] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:34,142] [INFO] Target genome list was writen to GCF_000264945.2_ASM26494v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:34,154] [INFO] Task started: fastANI
[2024-01-24 13:37:34,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg955e14f6-9d16-4902-9605-52409afa899c/GCF_000264945.2_ASM26494v2_genomic.fna.gz --refList GCF_000264945.2_ASM26494v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000264945.2_ASM26494v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:46,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:46,699] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:46,699] [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_000264945.2	s__Sphingobium indicum	100.0	1313	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	97.75	0.82	0.64	8	conclusive
GCF_004152845.1	s__Sphingobium fuliginis	91.6922	961	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_000722875.1	s__Sphingobium chlorophenolicum	89.6121	847	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.94	95.89	0.87	0.76	3	-
GCF_013375535.1	s__Sphingobium sp013375535	88.8046	868	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361945.1	s__Sphingobium barthaii_A	88.541	871	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005725.1	s__Sphingobium chungbukense	87.489	866	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.77	97.77	0.72	0.72	2	-
GCF_008692605.1	s__Sphingobium estronivorans	86.4882	776	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	86.3176	813	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873695.1	s__Sphingobium sp014873695	86.0262	855	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412635.1	s__Sphingobium bisphenolivorans	84.1376	756	1314	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:46,701] [INFO] GTDB search result was written to GCF_000264945.2_ASM26494v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:46,701] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:46,704] [INFO] DFAST_QC result json was written to GCF_000264945.2_ASM26494v2_genomic.fna/dqc_result.json
[2024-01-24 13:37:46,704] [INFO] DFAST_QC completed!
[2024-01-24 13:37:46,704] [INFO] Total running time: 0h1m19s