[2024-01-24 11:26:54,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,313] [INFO] DQC Reference Directory: /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference
[2024-01-24 11:26:58,218] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,221] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg7fbc95fa-dfeb-4d2f-9aae-74abce729629/GCF_901538385.1_ASM90153838v1_genomic.fna.gz | prodigal -d GCF_901538385.1_ASM90153838v1_genomic.fna/cds.fna -a GCF_901538385.1_ASM90153838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:25,702] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:25,702] [INFO] Task started: HMMsearch
[2024-01-24 11:27:25,702] [INFO] Running command: hmmsearch --tblout GCF_901538385.1_ASM90153838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/reference_markers.hmm GCF_901538385.1_ASM90153838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:26,077] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:26,079] [INFO] Found 6/6 markers.
[2024-01-24 11:27:26,148] [INFO] Query marker FASTA was written to GCF_901538385.1_ASM90153838v1_genomic.fna/markers.fasta
[2024-01-24 11:27:26,149] [INFO] Task started: Blastn
[2024-01-24 11:27:26,149] [INFO] Running command: blastn -query GCF_901538385.1_ASM90153838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/reference_markers.fasta -out GCF_901538385.1_ASM90153838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:26,812] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:26,816] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:26,816] [INFO] Target genome list was writen to GCF_901538385.1_ASM90153838v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:26,825] [INFO] Task started: fastANI
[2024-01-24 11:27:26,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbc95fa-dfeb-4d2f-9aae-74abce729629/GCF_901538385.1_ASM90153838v1_genomic.fna.gz --refList GCF_901538385.1_ASM90153838v1_genomic.fna/target_genomes.txt --output GCF_901538385.1_ASM90153838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:56,170] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:56,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:56,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:56,184] [INFO] Found 14 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:27:56,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:56,184] [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
Gemmata obscuriglobus		GCA_901538385.1	114	114	type	True	100.0	3010	3010	95	conclusive
Gemmata obscuriglobus	strain=DSM 5831	GCA_003149495.1	114	114	type	True	99.9977	2997	3010	95	conclusive
Gemmata obscuriglobus	strain=DSM 5831	GCA_008065095.1	114	114	type	True	99.9976	2997	3010	95	conclusive
Gemmata obscuriglobus	strain=UQM 2246	GCA_000171775.1	114	114	type	True	99.7881	2608	3010	95	conclusive
Urbifossiella limnaea	strain=ETA_A1	GCA_007747215.1	2528023	2528023	type	True	78.1355	964	3010	95	below_threshold
Fimbriiglobus ruber	strain=SP5	GCA_002197845.1	1908690	1908690	type	True	76.6988	619	3010	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.9586	170	3010	95	below_threshold
Dietzia timorensis	strain=ID05-A0528	GCA_001659785.1	499555	499555	type	True	74.944	53	3010	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.9131	196	3010	95	below_threshold
Propioniciclava soli	strain=YIM S02567	GCA_014858005.1	2775081	2775081	type	True	74.884	102	3010	95	below_threshold
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	74.8256	86	3010	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	74.7917	115	3010	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	74.7802	69	3010	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	74.7052	169	3010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:56,186] [INFO] DFAST Taxonomy check result was written to GCF_901538385.1_ASM90153838v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:56,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:56,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:56,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/checkm_data
[2024-01-24 11:27:56,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:56,274] [INFO] Task started: CheckM
[2024-01-24 11:27:56,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_901538385.1_ASM90153838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_901538385.1_ASM90153838v1_genomic.fna/checkm_input GCF_901538385.1_ASM90153838v1_genomic.fna/checkm_result
[2024-01-24 11:29:11,653] [INFO] Task succeeded: CheckM
[2024-01-24 11:29:11,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:29:11,683] [INFO] ===== Completeness check finished =====
[2024-01-24 11:29:11,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:29:11,684] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_901538385.1_ASM90153838v1_genomic.fna/markers.fasta)
[2024-01-24 11:29:11,684] [INFO] Task started: Blastn
[2024-01-24 11:29:11,684] [INFO] Running command: blastn -query GCF_901538385.1_ASM90153838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293cda2b-0607-4dfa-9a5f-4dd7f71a88c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_901538385.1_ASM90153838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:29:12,617] [INFO] Task succeeded: Blastn
[2024-01-24 11:29:12,621] [INFO] Selected 11 target genomes.
[2024-01-24 11:29:12,621] [INFO] Target genome list was writen to GCF_901538385.1_ASM90153838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:29:12,631] [INFO] Task started: fastANI
[2024-01-24 11:29:12,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fbc95fa-dfeb-4d2f-9aae-74abce729629/GCF_901538385.1_ASM90153838v1_genomic.fna.gz --refList GCF_901538385.1_ASM90153838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_901538385.1_ASM90153838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:29:37,053] [INFO] Task succeeded: fastANI
[2024-01-24 11:29:37,065] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:29:37,065] [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_008065095.1	s__Gemmata obscuriglobus	99.9976	2997	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.98	99.95	1.00	1.00	4	conclusive
GCF_017939745.1	s__Gemmata sp017939745	80.0691	1499	3010	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	79.896	1030	3010	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	79.8633	1402	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	97.81	97.81	0.89	0.89	2	-
GCF_901538265.1	s__Gemmata massiliana_A	79.775	1403	3010	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	79.769	1380	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872595.1	s__Gemmata sp016872595	79.5512	1075	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_901538445.1	s__Gemmata sp901538445	79.1554	1128	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005772955.1	s__Gemmata sp005772955	78.9827	986	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	99.91	99.90	0.94	0.93	4	-
GCA_005773755.1	s__Gemmata sp005773755	78.9802	766	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Gemmata	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	78.177	954	3010	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:29:37,066] [INFO] GTDB search result was written to GCF_901538385.1_ASM90153838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:29:37,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:29:37,073] [INFO] DFAST_QC result json was written to GCF_901538385.1_ASM90153838v1_genomic.fna/dqc_result.json
[2024-01-24 11:29:37,073] [INFO] DFAST_QC completed!
[2024-01-24 11:29:37,073] [INFO] Total running time: 0h2m43s