[2024-01-24 15:18:25,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:25,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:25,623] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference
[2024-01-24 15:18:26,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:26,939] [INFO] Task started: Prodigal
[2024-01-24 15:18:26,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgef921574-9618-4293-95eb-d074eaed57cc/GCF_000971175.1_ASM97117v1_genomic.fna.gz | prodigal -d GCF_000971175.1_ASM97117v1_genomic.fna/cds.fna -a GCF_000971175.1_ASM97117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:35,346] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:35,346] [INFO] Task started: HMMsearch
[2024-01-24 15:18:35,346] [INFO] Running command: hmmsearch --tblout GCF_000971175.1_ASM97117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/reference_markers.hmm GCF_000971175.1_ASM97117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:35,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:35,654] [INFO] Found 6/6 markers.
[2024-01-24 15:18:35,681] [INFO] Query marker FASTA was written to GCF_000971175.1_ASM97117v1_genomic.fna/markers.fasta
[2024-01-24 15:18:35,681] [INFO] Task started: Blastn
[2024-01-24 15:18:35,681] [INFO] Running command: blastn -query GCF_000971175.1_ASM97117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/reference_markers.fasta -out GCF_000971175.1_ASM97117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:37,126] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:37,129] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:37,130] [INFO] Target genome list was writen to GCF_000971175.1_ASM97117v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:37,161] [INFO] Task started: fastANI
[2024-01-24 15:18:37,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgef921574-9618-4293-95eb-d074eaed57cc/GCF_000971175.1_ASM97117v1_genomic.fna.gz --refList GCF_000971175.1_ASM97117v1_genomic.fna/target_genomes.txt --output GCF_000971175.1_ASM97117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:47,831] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:47,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:47,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:47,846] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:47,846] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:47,846] [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 pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	100.0	889	890	95	conclusive
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	83.5466	570	890	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	83.5251	619	890	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	83.3358	609	890	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	83.3009	563	890	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	83.2241	579	890	95	below_threshold
Demequina mangrovi	strain=DSM 24868	GCA_900109245.1	1043493	1043493	type	True	83.0509	589	890	95	below_threshold
Demequina mangrovi	strain=NBRC 105856	GCA_000759715.1	1043493	1043493	type	True	83.0397	586	890	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	82.9651	567	890	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	82.7581	587	890	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.1459	361	890	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.0899	373	890	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.9669	273	890	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.9606	349	890	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.7945	332	890	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:47,848] [INFO] DFAST Taxonomy check result was written to GCF_000971175.1_ASM97117v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:47,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:47,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:47,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/checkm_data
[2024-01-24 15:18:47,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:47,878] [INFO] Task started: CheckM
[2024-01-24 15:18:47,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000971175.1_ASM97117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000971175.1_ASM97117v1_genomic.fna/checkm_input GCF_000971175.1_ASM97117v1_genomic.fna/checkm_result
[2024-01-24 15:19:30,128] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:30,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:30,157] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:30,157] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:30,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000971175.1_ASM97117v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:30,158] [INFO] Task started: Blastn
[2024-01-24 15:19:30,158] [INFO] Running command: blastn -query GCF_000971175.1_ASM97117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7a0662a-22b5-4bbb-972c-9b98b70436a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000971175.1_ASM97117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:32,225] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:32,230] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:32,230] [INFO] Target genome list was writen to GCF_000971175.1_ASM97117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:32,237] [INFO] Task started: fastANI
[2024-01-24 15:19:32,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgef921574-9618-4293-95eb-d074eaed57cc/GCF_000971175.1_ASM97117v1_genomic.fna.gz --refList GCF_000971175.1_ASM97117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000971175.1_ASM97117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:38,466] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:38,482] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:38,482] [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_000971175.1	s__Demequina pelophila	100.0	889	890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000971255.1	s__Demequina rhizosphaerae	83.579	615	890	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	83.4908	574	890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971155.1	s__Demequina maris	83.2961	612	890	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971135.1	s__Demequina phytophila	83.2782	565	890	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	83.2273	579	890	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	83.0548	585	890	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	82.891	572	890	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	82.7574	588	890	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 15:19:38,484] [INFO] GTDB search result was written to GCF_000971175.1_ASM97117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:38,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:38,488] [INFO] DFAST_QC result json was written to GCF_000971175.1_ASM97117v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:38,488] [INFO] DFAST_QC completed!
[2024-01-24 15:19:38,488] [INFO] Total running time: 0h1m13s