[2024-01-24 12:44:10,086] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,091] [INFO] DQC Reference Directory: /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference
[2024-01-24 12:44:11,499] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:11,500] [INFO] Task started: Prodigal
[2024-01-24 12:44:11,500] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ec53351-fe2c-4969-b3ab-9c858fcd762d/GCF_000975075.1_ASM97507v1_genomic.fna.gz | prodigal -d GCF_000975075.1_ASM97507v1_genomic.fna/cds.fna -a GCF_000975075.1_ASM97507v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:20,231] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:20,231] [INFO] Task started: HMMsearch
[2024-01-24 12:44:20,231] [INFO] Running command: hmmsearch --tblout GCF_000975075.1_ASM97507v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/reference_markers.hmm GCF_000975075.1_ASM97507v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:20,486] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:20,487] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7ec53351-fe2c-4969-b3ab-9c858fcd762d/GCF_000975075.1_ASM97507v1_genomic.fna.gz]
[2024-01-24 12:44:20,513] [INFO] Query marker FASTA was written to GCF_000975075.1_ASM97507v1_genomic.fna/markers.fasta
[2024-01-24 12:44:20,514] [INFO] Task started: Blastn
[2024-01-24 12:44:20,514] [INFO] Running command: blastn -query GCF_000975075.1_ASM97507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/reference_markers.fasta -out GCF_000975075.1_ASM97507v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:21,357] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:21,360] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:21,361] [INFO] Target genome list was writen to GCF_000975075.1_ASM97507v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:21,404] [INFO] Task started: fastANI
[2024-01-24 12:44:21,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec53351-fe2c-4969-b3ab-9c858fcd762d/GCF_000975075.1_ASM97507v1_genomic.fna.gz --refList GCF_000975075.1_ASM97507v1_genomic.fna/target_genomes.txt --output GCF_000975075.1_ASM97507v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:30,594] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:30,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:30,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:30,609] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:30,609] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:30,610] [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
Demequina lutea	strain=DSM 19970	GCA_013409005.1	431489	431489	type	True	99.9993	855	857	95	conclusive
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	78.8952	241	857	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	78.8917	246	857	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	78.8721	245	857	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	78.7892	238	857	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	78.7599	226	857	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	78.7484	253	857	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	78.6911	245	857	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	78.6779	240	857	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	78.4605	250	857	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	78.4578	225	857	95	below_threshold
Demequina oxidasica	strain=NBRC 106264	GCA_000975115.1	676199	676199	type	True	77.9114	151	857	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.284	174	857	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.2248	154	857	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.1254	149	857	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.9384	163	857	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	76.6433	78	857	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:30,612] [INFO] DFAST Taxonomy check result was written to GCF_000975075.1_ASM97507v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:30,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:30,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:30,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/checkm_data
[2024-01-24 12:44:30,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:30,646] [INFO] Task started: CheckM
[2024-01-24 12:44:30,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000975075.1_ASM97507v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000975075.1_ASM97507v1_genomic.fna/checkm_input GCF_000975075.1_ASM97507v1_genomic.fna/checkm_result
[2024-01-24 12:45:00,405] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:00,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:00,429] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:00,429] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:00,429] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000975075.1_ASM97507v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:00,430] [INFO] Task started: Blastn
[2024-01-24 12:45:00,430] [INFO] Running command: blastn -query GCF_000975075.1_ASM97507v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5a809ed-f4ab-4e09-8419-f65399db7687/dqc_reference/reference_markers_gtdb.fasta -out GCF_000975075.1_ASM97507v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:01,723] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:01,727] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:01,727] [INFO] Target genome list was writen to GCF_000975075.1_ASM97507v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:01,752] [INFO] Task started: fastANI
[2024-01-24 12:45:01,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ec53351-fe2c-4969-b3ab-9c858fcd762d/GCF_000975075.1_ASM97507v1_genomic.fna.gz --refList GCF_000975075.1_ASM97507v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000975075.1_ASM97507v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:09,517] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:09,530] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:09,530] [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_013409005.1	s__Demequina lutea	99.9993	855	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_016278775.1	s__Demequina sp016278775	79.149	282	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759715.1	s__Demequina mangrovi	78.8582	243	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971155.1	s__Demequina maris	78.8542	246	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971235.1	s__Demequina subtropica	78.8069	237	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971195.1	s__Demequina soli	78.7315	254	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971135.1	s__Demequina phytophila	78.6955	230	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971255.1	s__Demequina rhizosphaerae	78.6569	247	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_000971215.1	s__Demequina silvatica	78.4769	249	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090115.1	s__Demequina sp002090115	78.4385	243	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971175.1	s__Demequina pelophila	78.4068	228	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000975095.1	s__Demequina aestuarii	78.193	192	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090095.1	s__Demequina sp002090095	78.1865	187	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090055.1	s__Demequina sp002090055	78.1795	214	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090175.1	s__Demequina sp002090175	78.1011	225	857	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:09,533] [INFO] GTDB search result was written to GCF_000975075.1_ASM97507v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:09,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:09,540] [INFO] DFAST_QC result json was written to GCF_000975075.1_ASM97507v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:09,541] [INFO] DFAST_QC completed!
[2024-01-24 12:45:09,541] [INFO] Total running time: 0h0m59s