[2024-01-24 14:54:49,681] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,683] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,683] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference
[2024-01-24 14:54:50,933] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,933] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,934] [INFO] Running command: gunzip -c /var/lib/cwl/stg80757438-8c09-4455-b151-6aed67e44e83/GCF_004346265.1_ASM434626v1_genomic.fna.gz | prodigal -d GCF_004346265.1_ASM434626v1_genomic.fna/cds.fna -a GCF_004346265.1_ASM434626v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:58,905] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:58,906] [INFO] Task started: HMMsearch
[2024-01-24 14:54:58,906] [INFO] Running command: hmmsearch --tblout GCF_004346265.1_ASM434626v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/reference_markers.hmm GCF_004346265.1_ASM434626v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:59,135] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:59,136] [INFO] Found 6/6 markers.
[2024-01-24 14:54:59,161] [INFO] Query marker FASTA was written to GCF_004346265.1_ASM434626v1_genomic.fna/markers.fasta
[2024-01-24 14:54:59,162] [INFO] Task started: Blastn
[2024-01-24 14:54:59,162] [INFO] Running command: blastn -query GCF_004346265.1_ASM434626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/reference_markers.fasta -out GCF_004346265.1_ASM434626v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:00,194] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:00,197] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:00,197] [INFO] Target genome list was writen to GCF_004346265.1_ASM434626v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:00,204] [INFO] Task started: fastANI
[2024-01-24 14:55:00,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg80757438-8c09-4455-b151-6aed67e44e83/GCF_004346265.1_ASM434626v1_genomic.fna.gz --refList GCF_004346265.1_ASM434626v1_genomic.fna/target_genomes.txt --output GCF_004346265.1_ASM434626v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:10,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:10,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:10,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:10,185] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:55:10,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:10,186] [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	100.0	850	851	95	conclusive
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	99.9389	806	851	95	conclusive
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	85.62	684	851	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	84.4076	621	851	95	below_threshold
Thermomonas hydrothermalis	strain=DSM 14834	GCA_900129205.1	213588	213588	type	True	83.4851	586	851	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.8275	532	851	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	82.3827	606	851	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	82.2427	488	851	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	81.6961	524	851	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.631	565	851	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.6167	529	851	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.4749	521	851	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.8728	501	851	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	80.8704	482	851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:10,190] [INFO] DFAST Taxonomy check result was written to GCF_004346265.1_ASM434626v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:10,190] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:10,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:10,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/checkm_data
[2024-01-24 14:55:10,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:10,217] [INFO] Task started: CheckM
[2024-01-24 14:55:10,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004346265.1_ASM434626v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004346265.1_ASM434626v1_genomic.fna/checkm_input GCF_004346265.1_ASM434626v1_genomic.fna/checkm_result
[2024-01-24 14:55:41,071] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:41,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:41,087] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:41,087] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:41,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004346265.1_ASM434626v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:41,088] [INFO] Task started: Blastn
[2024-01-24 14:55:41,088] [INFO] Running command: blastn -query GCF_004346265.1_ASM434626v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f8a24c-1187-406f-9467-855d78a0834d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004346265.1_ASM434626v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:43,158] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:43,163] [INFO] Selected 10 target genomes.
[2024-01-24 14:55:43,163] [INFO] Target genome list was writen to GCF_004346265.1_ASM434626v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:43,177] [INFO] Task started: fastANI
[2024-01-24 14:55:43,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg80757438-8c09-4455-b151-6aed67e44e83/GCF_004346265.1_ASM434626v1_genomic.fna.gz --refList GCF_004346265.1_ASM434626v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004346265.1_ASM434626v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:50,456] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:50,471] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:50,472] [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	100.0	850	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	conclusive
GCA_017305095.1	s__Thermomonas sp017305095	93.1173	746	851	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	86.611	683	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014678725.1	s__Thermomonas sp014678725	85.9119	679	851	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	85.6407	683	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_006337105.1	s__Thermomonas sp006337105	84.4045	621	851	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	84.2517	522	851	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	83.8767	402	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	81.7043	523	851	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	81.6038	530	851	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 14:55:50,477] [INFO] GTDB search result was written to GCF_004346265.1_ASM434626v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:50,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:50,482] [INFO] DFAST_QC result json was written to GCF_004346265.1_ASM434626v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:50,482] [INFO] DFAST_QC completed!
[2024-01-24 14:55:50,482] [INFO] Total running time: 0h1m1s