[2024-01-24 11:20:04,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:04,116] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:04,116] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference
[2024-01-24 11:20:05,306] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:05,307] [INFO] Task started: Prodigal
[2024-01-24 11:20:05,307] [INFO] Running command: gunzip -c /var/lib/cwl/stg3349bc62-58ee-4388-906e-d87091b4393d/GCF_000975095.1_ASM97509v1_genomic.fna.gz | prodigal -d GCF_000975095.1_ASM97509v1_genomic.fna/cds.fna -a GCF_000975095.1_ASM97509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:13,992] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:13,993] [INFO] Task started: HMMsearch
[2024-01-24 11:20:13,993] [INFO] Running command: hmmsearch --tblout GCF_000975095.1_ASM97509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/reference_markers.hmm GCF_000975095.1_ASM97509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:14,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:14,185] [INFO] Found 6/6 markers.
[2024-01-24 11:20:14,207] [INFO] Query marker FASTA was written to GCF_000975095.1_ASM97509v1_genomic.fna/markers.fasta
[2024-01-24 11:20:14,208] [INFO] Task started: Blastn
[2024-01-24 11:20:14,208] [INFO] Running command: blastn -query GCF_000975095.1_ASM97509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/reference_markers.fasta -out GCF_000975095.1_ASM97509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:15,277] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:15,281] [INFO] Selected 19 target genomes.
[2024-01-24 11:20:15,281] [INFO] Target genome list was writen to GCF_000975095.1_ASM97509v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:15,320] [INFO] Task started: fastANI
[2024-01-24 11:20:15,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg3349bc62-58ee-4388-906e-d87091b4393d/GCF_000975095.1_ASM97509v1_genomic.fna.gz --refList GCF_000975095.1_ASM97509v1_genomic.fna/target_genomes.txt --output GCF_000975095.1_ASM97509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:26,505] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:26,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:26,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:26,520] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:26,520] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:26,521] [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 activiva	strain=NBRC 110675	GCA_016862815.1	1582364	1582364	type	True	81.4141	540	928	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	80.2491	428	928	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	80.1777	414	928	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	80.13	433	928	95	below_threshold
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	80.0207	438	928	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	79.9031	418	928	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	79.892	430	928	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	79.8866	417	928	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	79.8057	398	928	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	79.4229	377	928	95	below_threshold
Demequina globuliformis	strain=NBRC 106266	GCA_000975155.1	676202	676202	type	True	79.063	327	928	95	below_threshold
Demequina flava	strain=NBRC 105854	GCA_000975035.1	1095025	1095025	type	True	78.9211	314	928	95	below_threshold
Actinotalea subterranea	strain=HO-Ch2	GCA_008364845.1	2607497	2607497	type	True	77.7297	243	928	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.689	246	928	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.3769	190	928	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	77.0195	148	928	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	76.861	144	928	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	76.3183	152	928	95	below_threshold
Microbispora rosea subsp. rosea	strain=NBRC 14044	GCA_016863055.1	58118	58117	type	True	75.9778	159	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:26,522] [INFO] DFAST Taxonomy check result was written to GCF_000975095.1_ASM97509v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:26,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:26,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:26,523] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/checkm_data
[2024-01-24 11:20:26,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:26,551] [INFO] Task started: CheckM
[2024-01-24 11:20:26,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000975095.1_ASM97509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000975095.1_ASM97509v1_genomic.fna/checkm_input GCF_000975095.1_ASM97509v1_genomic.fna/checkm_result
[2024-01-24 11:21:03,128] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:03,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:03,146] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:03,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:03,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000975095.1_ASM97509v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:03,147] [INFO] Task started: Blastn
[2024-01-24 11:21:03,148] [INFO] Running command: blastn -query GCF_000975095.1_ASM97509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9e809cc-2b5a-4735-a5c0-f271103c2673/dqc_reference/reference_markers_gtdb.fasta -out GCF_000975095.1_ASM97509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:04,792] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:04,795] [INFO] Selected 9 target genomes.
[2024-01-24 11:21:04,795] [INFO] Target genome list was writen to GCF_000975095.1_ASM97509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:04,802] [INFO] Task started: fastANI
[2024-01-24 11:21:04,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg3349bc62-58ee-4388-906e-d87091b4393d/GCF_000975095.1_ASM97509v1_genomic.fna.gz --refList GCF_000975095.1_ASM97509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000975095.1_ASM97509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:09,802] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:09,810] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:09,810] [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_000975095.1	s__Demequina aestuarii	100.0	927	928	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_016862815.1	s__Demequina activiva	81.4265	539	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090155.1	s__Demequina sp002090155	81.1059	540	928	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	80.7996	496	928	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	80.2259	420	928	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	80.1773	446	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090135.1	s__Demequina sp002090135	80.089	431	928	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	79.986	438	928	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_000971175.1	s__Demequina pelophila	79.8768	420	928	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 11:21:09,812] [INFO] GTDB search result was written to GCF_000975095.1_ASM97509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:09,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:09,816] [INFO] DFAST_QC result json was written to GCF_000975095.1_ASM97509v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:09,816] [INFO] DFAST_QC completed!
[2024-01-24 11:21:09,816] [INFO] Total running time: 0h1m6s