[2024-01-24 10:57:13,237] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:13,239] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:13,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference
[2024-01-24 10:57:14,690] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:14,691] [INFO] Task started: Prodigal
[2024-01-24 10:57:14,691] [INFO] Running command: gunzip -c /var/lib/cwl/stg64747591-e248-42f1-86dd-12b41285bcea/GCF_004363655.1_ASM436365v1_genomic.fna.gz | prodigal -d GCF_004363655.1_ASM436365v1_genomic.fna/cds.fna -a GCF_004363655.1_ASM436365v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:39,248] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:39,248] [INFO] Task started: HMMsearch
[2024-01-24 10:57:39,248] [INFO] Running command: hmmsearch --tblout GCF_004363655.1_ASM436365v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/reference_markers.hmm GCF_004363655.1_ASM436365v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:39,643] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:39,644] [INFO] Found 6/6 markers.
[2024-01-24 10:57:39,707] [INFO] Query marker FASTA was written to GCF_004363655.1_ASM436365v1_genomic.fna/markers.fasta
[2024-01-24 10:57:39,708] [INFO] Task started: Blastn
[2024-01-24 10:57:39,708] [INFO] Running command: blastn -query GCF_004363655.1_ASM436365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/reference_markers.fasta -out GCF_004363655.1_ASM436365v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:40,658] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:40,661] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:40,662] [INFO] Target genome list was writen to GCF_004363655.1_ASM436365v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:40,670] [INFO] Task started: fastANI
[2024-01-24 10:57:40,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg64747591-e248-42f1-86dd-12b41285bcea/GCF_004363655.1_ASM436365v1_genomic.fna.gz --refList GCF_004363655.1_ASM436365v1_genomic.fna/target_genomes.txt --output GCF_004363655.1_ASM436365v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:00,348] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:00,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:00,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:00,365] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:00,366] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:00,366] [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
Tahibacter aquaticus	strain=DSM 21667	GCA_004363655.1	520092	520092	type	True	100.0	2375	2378	95	conclusive
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	82.6939	1027	2378	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	78.168	418	2378	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	78.0982	441	2378	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	78.0615	396	2378	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	78.004	417	2378	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	77.922	420	2378	95	below_threshold
Dokdonella immobilis	strain=CGMCC 1.7659	GCA_900115085.1	578942	578942	type	True	77.918	460	2378	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	77.908	558	2378	95	below_threshold
Dokdonella fugitiva	strain=A3	GCA_004342425.1	328517	328517	type	True	77.7668	519	2378	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	77.7202	516	2378	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	77.6424	587	2378	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	77.5876	413	2378	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	77.5815	393	2378	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	77.5232	363	2378	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	77.45	409	2378	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	77.4313	508	2378	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	77.3802	358	2378	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	77.2975	471	2378	95	below_threshold
Pseudolysobacter antarcticus	strain=AQ6-296	GCA_004168365.1	2511995	2511995	type	True	76.8964	301	2378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:00,367] [INFO] DFAST Taxonomy check result was written to GCF_004363655.1_ASM436365v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:00,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:00,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:00,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/checkm_data
[2024-01-24 10:58:00,370] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:00,438] [INFO] Task started: CheckM
[2024-01-24 10:58:00,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363655.1_ASM436365v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363655.1_ASM436365v1_genomic.fna/checkm_input GCF_004363655.1_ASM436365v1_genomic.fna/checkm_result
[2024-01-24 10:59:07,301] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:07,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,323] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:07,324] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:07,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363655.1_ASM436365v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:07,324] [INFO] Task started: Blastn
[2024-01-24 10:59:07,325] [INFO] Running command: blastn -query GCF_004363655.1_ASM436365v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5758e7-8fe8-49c3-b1b4-272c3d24f8c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363655.1_ASM436365v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,035] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,039] [INFO] Selected 12 target genomes.
[2024-01-24 10:59:09,040] [INFO] Target genome list was writen to GCF_004363655.1_ASM436365v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,049] [INFO] Task started: fastANI
[2024-01-24 10:59:09,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg64747591-e248-42f1-86dd-12b41285bcea/GCF_004363655.1_ASM436365v1_genomic.fna.gz --refList GCF_004363655.1_ASM436365v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363655.1_ASM436365v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:21,613] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:21,626] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:21,626] [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_004363655.1	s__Tahibacter aquaticus	100.0	2375	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001725155.1	s__Tahibacter sp001725155	82.4413	1278	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	99.99	99.99	0.99	0.98	4	-
GCA_013298265.1	s__Tahibacter sp013298265	82.0893	793	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790075.1	s__Tahibacter sp016790075	80.3449	909	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Tahibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	78.4618	525	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744955.1	s__Dokdonella_A sp017744955	78.1933	632	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632775.1	s__Dokdonella koreensis	77.9363	554	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115085.1	s__Dokdonella immobilis	77.918	460	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241385.1	s__Dokdonella denitrificans_A	77.8311	548	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	77.796	448	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCA_018242445.1	s__SZAS-103 sp018242445	77.5018	313	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003497545.1	s__Arenimonas sp003497545	77.4894	309	2378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.43	99.43	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:21,628] [INFO] GTDB search result was written to GCF_004363655.1_ASM436365v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:21,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:21,632] [INFO] DFAST_QC result json was written to GCF_004363655.1_ASM436365v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:21,632] [INFO] DFAST_QC completed!
[2024-01-24 10:59:21,632] [INFO] Total running time: 0h2m8s