[2024-01-24 12:23:03,974] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,976] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,976] [INFO] DQC Reference Directory: /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference
[2024-01-24 12:23:05,290] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,291] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,291] [INFO] Running command: gunzip -c /var/lib/cwl/stg99c81394-3bd0-48f3-913f-37ac195401cb/GCF_022419185.1_ASM2241918v1_genomic.fna.gz | prodigal -d GCF_022419185.1_ASM2241918v1_genomic.fna/cds.fna -a GCF_022419185.1_ASM2241918v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:12,639] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:12,640] [INFO] Task started: HMMsearch
[2024-01-24 12:23:12,640] [INFO] Running command: hmmsearch --tblout GCF_022419185.1_ASM2241918v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/reference_markers.hmm GCF_022419185.1_ASM2241918v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:12,876] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:12,877] [INFO] Found 6/6 markers.
[2024-01-24 12:23:12,904] [INFO] Query marker FASTA was written to GCF_022419185.1_ASM2241918v1_genomic.fna/markers.fasta
[2024-01-24 12:23:12,904] [INFO] Task started: Blastn
[2024-01-24 12:23:12,904] [INFO] Running command: blastn -query GCF_022419185.1_ASM2241918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/reference_markers.fasta -out GCF_022419185.1_ASM2241918v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:14,004] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:14,007] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:14,007] [INFO] Target genome list was writen to GCF_022419185.1_ASM2241918v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:14,012] [INFO] Task started: fastANI
[2024-01-24 12:23:14,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c81394-3bd0-48f3-913f-37ac195401cb/GCF_022419185.1_ASM2241918v1_genomic.fna.gz --refList GCF_022419185.1_ASM2241918v1_genomic.fna/target_genomes.txt --output GCF_022419185.1_ASM2241918v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:25,111] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:25,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:25,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:25,128] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:25,128] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:25,128] [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
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	87.1335	603	832	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	86.9099	602	832	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	83.8277	620	832	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	83.6427	584	832	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	83.4452	556	832	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	82.6568	560	832	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.5623	484	832	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	82.0321	566	832	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	81.7821	584	832	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.6996	526	832	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	81.6485	557	832	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	81.5846	547	832	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.4272	532	832	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.2898	568	832	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.063	548	832	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:25,130] [INFO] DFAST Taxonomy check result was written to GCF_022419185.1_ASM2241918v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:25,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:25,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:25,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/checkm_data
[2024-01-24 12:23:25,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:25,167] [INFO] Task started: CheckM
[2024-01-24 12:23:25,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022419185.1_ASM2241918v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022419185.1_ASM2241918v1_genomic.fna/checkm_input GCF_022419185.1_ASM2241918v1_genomic.fna/checkm_result
[2024-01-24 12:24:02,187] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:02,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:02,208] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:02,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:02,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022419185.1_ASM2241918v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:02,209] [INFO] Task started: Blastn
[2024-01-24 12:24:02,209] [INFO] Running command: blastn -query GCF_022419185.1_ASM2241918v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge21b6c80-d763-43c5-9fc8-bef57713fdd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_022419185.1_ASM2241918v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:04,341] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:04,345] [INFO] Selected 11 target genomes.
[2024-01-24 12:24:04,345] [INFO] Target genome list was writen to GCF_022419185.1_ASM2241918v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:04,352] [INFO] Task started: fastANI
[2024-01-24 12:24:04,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c81394-3bd0-48f3-913f-37ac195401cb/GCF_022419185.1_ASM2241918v1_genomic.fna.gz --refList GCF_022419185.1_ASM2241918v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022419185.1_ASM2241918v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:12,042] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:12,056] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:12,057] [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_004346265.1	s__Thermomonas haemolytica	87.091	605	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_017305095.1	s__Thermomonas sp017305095	86.9256	620	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	84.3089	546	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	83.9979	612	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302095.1	s__Thermomonas sp017302095	83.9164	424	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337105.1	s__Thermomonas sp006337105	83.8055	622	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	83.6368	583	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_014678725.1	s__Thermomonas sp014678725	83.626	580	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	81.9562	544	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_014652935.1	s__Luteimonas padinae	81.7142	525	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.587	522	832	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:12,060] [INFO] GTDB search result was written to GCF_022419185.1_ASM2241918v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:12,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:12,068] [INFO] DFAST_QC result json was written to GCF_022419185.1_ASM2241918v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:12,068] [INFO] DFAST_QC completed!
[2024-01-24 12:24:12,068] [INFO] Total running time: 0h1m8s