[2024-01-24 15:10:41,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,013] [INFO] DQC Reference Directory: /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference
[2024-01-24 15:10:42,385] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,386] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,386] [INFO] Running command: gunzip -c /var/lib/cwl/stg229050d7-bbb2-43ba-bbfa-494b11db1d41/GCF_030296675.1_ASM3029667v1_genomic.fna.gz | prodigal -d GCF_030296675.1_ASM3029667v1_genomic.fna/cds.fna -a GCF_030296675.1_ASM3029667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:51,279] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:51,279] [INFO] Task started: HMMsearch
[2024-01-24 15:10:51,279] [INFO] Running command: hmmsearch --tblout GCF_030296675.1_ASM3029667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/reference_markers.hmm GCF_030296675.1_ASM3029667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:51,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:51,550] [INFO] Found 6/6 markers.
[2024-01-24 15:10:51,579] [INFO] Query marker FASTA was written to GCF_030296675.1_ASM3029667v1_genomic.fna/markers.fasta
[2024-01-24 15:10:51,580] [INFO] Task started: Blastn
[2024-01-24 15:10:51,580] [INFO] Running command: blastn -query GCF_030296675.1_ASM3029667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/reference_markers.fasta -out GCF_030296675.1_ASM3029667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:52,898] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:52,909] [INFO] Selected 16 target genomes.
[2024-01-24 15:10:52,910] [INFO] Target genome list was writen to GCF_030296675.1_ASM3029667v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:52,914] [INFO] Task started: fastANI
[2024-01-24 15:10:52,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg229050d7-bbb2-43ba-bbfa-494b11db1d41/GCF_030296675.1_ASM3029667v1_genomic.fna.gz --refList GCF_030296675.1_ASM3029667v1_genomic.fna/target_genomes.txt --output GCF_030296675.1_ASM3029667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:03,980] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:03,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:03,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:03,994] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:03,994] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:03,994] [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 maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	83.506	603	901	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	83.4589	611	901	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	83.4409	591	901	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	83.4013	614	901	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	83.3581	589	901	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	83.0504	586	901	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	83.019	600	901	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	82.9693	603	901	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	82.9607	591	901	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	82.6552	595	901	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	82.0359	527	901	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	78.3901	288	901	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.1591	331	901	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.9726	312	901	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.7847	358	901	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.7318	316	901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:03,996] [INFO] DFAST Taxonomy check result was written to GCF_030296675.1_ASM3029667v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:03,996] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:03,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:03,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/checkm_data
[2024-01-24 15:11:03,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:04,027] [INFO] Task started: CheckM
[2024-01-24 15:11:04,027] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030296675.1_ASM3029667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030296675.1_ASM3029667v1_genomic.fna/checkm_input GCF_030296675.1_ASM3029667v1_genomic.fna/checkm_result
[2024-01-24 15:11:40,173] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:40,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:40,195] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:40,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:40,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030296675.1_ASM3029667v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:40,197] [INFO] Task started: Blastn
[2024-01-24 15:11:40,197] [INFO] Running command: blastn -query GCF_030296675.1_ASM3029667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc841669d-c177-42ca-a214-19b74b1a0317/dqc_reference/reference_markers_gtdb.fasta -out GCF_030296675.1_ASM3029667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:42,328] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:42,333] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:42,333] [INFO] Target genome list was writen to GCF_030296675.1_ASM3029667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:42,341] [INFO] Task started: fastANI
[2024-01-24 15:11:42,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg229050d7-bbb2-43ba-bbfa-494b11db1d41/GCF_030296675.1_ASM3029667v1_genomic.fna.gz --refList GCF_030296675.1_ASM3029667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030296675.1_ASM3029667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:49,147] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:49,162] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:11:49,162] [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_000971155.1	s__Demequina maris	83.4881	604	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971195.1	s__Demequina soli	83.4561	590	901	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	83.4444	613	901	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	83.4162	613	901	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	83.3731	588	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971235.1	s__Demequina subtropica	83.007	588	901	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	83.0011	601	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000971395.1	s__Demequina iriomotensis	82.9693	603	901	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971115.1	s__Demequina gelatinilytica	82.6551	595	901	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	82.0498	526	901	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 15:11:49,164] [INFO] GTDB search result was written to GCF_030296675.1_ASM3029667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:49,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:49,168] [INFO] DFAST_QC result json was written to GCF_030296675.1_ASM3029667v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:49,168] [INFO] DFAST_QC completed!
[2024-01-24 15:11:49,168] [INFO] Total running time: 0h1m8s