[2024-01-24 12:47:13,608] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:13,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:13,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference
[2024-01-24 12:47:14,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:14,930] [INFO] Task started: Prodigal
[2024-01-24 12:47:14,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b507b27-8fe4-4d8c-a800-ede3633c1555/GCF_008254045.1_ASM825404v1_genomic.fna.gz | prodigal -d GCF_008254045.1_ASM825404v1_genomic.fna/cds.fna -a GCF_008254045.1_ASM825404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:49,069] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:49,069] [INFO] Task started: HMMsearch
[2024-01-24 12:47:49,069] [INFO] Running command: hmmsearch --tblout GCF_008254045.1_ASM825404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/reference_markers.hmm GCF_008254045.1_ASM825404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:49,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:49,518] [INFO] Found 6/6 markers.
[2024-01-24 12:47:49,588] [INFO] Query marker FASTA was written to GCF_008254045.1_ASM825404v1_genomic.fna/markers.fasta
[2024-01-24 12:47:49,588] [INFO] Task started: Blastn
[2024-01-24 12:47:49,589] [INFO] Running command: blastn -query GCF_008254045.1_ASM825404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/reference_markers.fasta -out GCF_008254045.1_ASM825404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:50,303] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:50,306] [INFO] Selected 21 target genomes.
[2024-01-24 12:47:50,306] [INFO] Target genome list was writen to GCF_008254045.1_ASM825404v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:50,324] [INFO] Task started: fastANI
[2024-01-24 12:47:50,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b507b27-8fe4-4d8c-a800-ede3633c1555/GCF_008254045.1_ASM825404v1_genomic.fna.gz --refList GCF_008254045.1_ASM825404v1_genomic.fna/target_genomes.txt --output GCF_008254045.1_ASM825404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:15,672] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:15,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:15,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:15,691] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:15,691] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:15,691] [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
Limnoglobus roseus	strain=PX52	GCA_008254045.1	2598579	2598579	type	True	100.0	3123	3126	95	conclusive
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	77.1083	866	3126	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	77.0183	751	3126	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	76.9378	657	3126	95	below_threshold
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	76.9296	656	3126	95	below_threshold
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	76.9007	650	3126	95	below_threshold
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	76.8896	593	3126	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.984	176	3126	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.9621	173	3126	95	below_threshold
Variovorax boronicumulans	strain=NBRC 103145	GCA_001591345.1	436515	436515	type	True	74.8973	136	3126	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	74.8612	55	3126	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	74.8229	67	3126	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	74.8094	75	3126	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	74.7866	111	3126	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.7487	129	3126	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	74.7315	124	3126	95	below_threshold
Acidovorax konjaci	strain=DSM 7481	GCA_900112675.1	32040	32040	type	True	74.7315	80	3126	95	below_threshold
Streptoalloteichus tenebrarius	strain=DSM 40477	GCA_024171885.1	1933	1933	type	True	74.7047	182	3126	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	74.5966	57	3126	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	74.5696	118	3126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:15,693] [INFO] DFAST Taxonomy check result was written to GCF_008254045.1_ASM825404v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:15,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:15,693] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:15,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/checkm_data
[2024-01-24 12:48:15,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:15,781] [INFO] Task started: CheckM
[2024-01-24 12:48:15,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008254045.1_ASM825404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008254045.1_ASM825404v1_genomic.fna/checkm_input GCF_008254045.1_ASM825404v1_genomic.fna/checkm_result
[2024-01-24 12:49:43,780] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:43,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:43,806] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:43,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:43,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008254045.1_ASM825404v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:43,808] [INFO] Task started: Blastn
[2024-01-24 12:49:43,808] [INFO] Running command: blastn -query GCF_008254045.1_ASM825404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d9537da-8776-4d81-94e5-50058b68ebe0/dqc_reference/reference_markers_gtdb.fasta -out GCF_008254045.1_ASM825404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:44,725] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:44,730] [INFO] Selected 25 target genomes.
[2024-01-24 12:49:44,730] [INFO] Target genome list was writen to GCF_008254045.1_ASM825404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:44,771] [INFO] Task started: fastANI
[2024-01-24 12:49:44,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b507b27-8fe4-4d8c-a800-ede3633c1555/GCF_008254045.1_ASM825404v1_genomic.fna.gz --refList GCF_008254045.1_ASM825404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008254045.1_ASM825404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:50:14,936] [INFO] Task succeeded: fastANI
[2024-01-24 12:50:14,965] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:50:14,965] [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_008254045.1	s__Limnoglobus roseus	100.0	3125	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Limnoglobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016795225.1	s__Limnoglobus sp016795225	78.8016	660	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Limnoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	77.4447	795	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013128195.2	s__Gemmata tundricola	77.2845	712	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	77.1766	819	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	77.0432	598	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000531095.1	s__Gemmata massiliana	77.0381	543	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_002197845.1	s__Fimbriiglobus ruber	77.0326	739	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Fimbriiglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901538265.1	s__Gemmata massiliana_A	77.0242	585	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306025.1	s__Gemmata sp017306025	76.9967	567	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065095.1	s__Gemmata obscuriglobus	76.95	656	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	-
GCA_013822345.1	s__Gemmata sp013822345	76.5684	703	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692065.1	s__SIAQ01 sp009692065	75.5916	160	3126	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710335.1	s__JADJXQ01 sp016710335	75.064	67	3126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__JADJXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144865.1	s__Ramlibacter sp004144865	74.9803	80	3126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525745.1	s__PLA4 sp011525745	74.9526	98	3126	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__UTPLA1;g__PLA4	95.0	99.79	99.79	0.95	0.95	2	-
GCF_004364785.1	s__Novosphingobium sp004364785	74.7687	50	3126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014196495.1	s__Sphingobium jiangsuense	74.7651	70	3126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956315.1	s__Sphingomonas_G montana	74.6915	69	3126	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698095.1	s__CF-46 sp013698095	74.6601	73	3126	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__CF-46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026785.1	s__UBA5189 sp012026785	74.5744	89	3126	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__CSP1-4;g__UBA5189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:50:14,967] [INFO] GTDB search result was written to GCF_008254045.1_ASM825404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:50:14,967] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:50:14,971] [INFO] DFAST_QC result json was written to GCF_008254045.1_ASM825404v1_genomic.fna/dqc_result.json
[2024-01-24 12:50:14,971] [INFO] DFAST_QC completed!
[2024-01-24 12:50:14,971] [INFO] Total running time: 0h3m1s