[2024-01-25 18:50:50,612] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,614] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,614] [INFO] DQC Reference Directory: /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference
[2024-01-25 18:50:51,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,759] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bd77aec-bac8-405f-979b-f1f8fe33a10e/GCF_016862815.1_ASM1686281v1_genomic.fna.gz | prodigal -d GCF_016862815.1_ASM1686281v1_genomic.fna/cds.fna -a GCF_016862815.1_ASM1686281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:58,734] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:58,735] [INFO] Task started: HMMsearch
[2024-01-25 18:50:58,735] [INFO] Running command: hmmsearch --tblout GCF_016862815.1_ASM1686281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/reference_markers.hmm GCF_016862815.1_ASM1686281v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:58,930] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:58,931] [INFO] Found 6/6 markers.
[2024-01-25 18:50:58,952] [INFO] Query marker FASTA was written to GCF_016862815.1_ASM1686281v1_genomic.fna/markers.fasta
[2024-01-25 18:50:58,952] [INFO] Task started: Blastn
[2024-01-25 18:50:58,952] [INFO] Running command: blastn -query GCF_016862815.1_ASM1686281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/reference_markers.fasta -out GCF_016862815.1_ASM1686281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:00,093] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:00,096] [INFO] Selected 18 target genomes.
[2024-01-25 18:51:00,096] [INFO] Target genome list was writen to GCF_016862815.1_ASM1686281v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:00,111] [INFO] Task started: fastANI
[2024-01-25 18:51:00,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd77aec-bac8-405f-979b-f1f8fe33a10e/GCF_016862815.1_ASM1686281v1_genomic.fna.gz --refList GCF_016862815.1_ASM1686281v1_genomic.fna/target_genomes.txt --output GCF_016862815.1_ASM1686281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:11,014] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:11,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:11,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:11,027] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:11,027] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:11,027] [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	100.0	820	820	95	conclusive
Demequina rhizosphaerae	strain=NBRC 109397	GCA_000971255.1	1638985	1638985	type	True	80.8363	457	820	95	below_threshold
Demequina silvatica	strain=NBRC 109395	GCA_000971215.1	1638988	1638988	type	True	80.6973	479	820	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	80.6811	428	820	95	below_threshold
Demequina soli	strain=NBRC 109394	GCA_000971195.1	1638987	1638987	type	True	80.6609	452	820	95	below_threshold
Demequina maris	strain=NBRC 109392	GCA_000971155.1	1638982	1638982	type	True	80.6309	480	820	95	below_threshold
Demequina phytophila	strain=NBRC 109391	GCA_000971135.1	1638981	1638981	type	True	80.6285	461	820	95	below_threshold
Demequina iriomotensis	strain=NBRC 109399	GCA_000971395.1	1536641	1536641	type	True	80.4295	453	820	95	below_threshold
Demequina gelatinilytica	strain=NBRC 109390	GCA_000971115.1	1638980	1638980	type	True	80.4044	455	820	95	below_threshold
Demequina subtropica	strain=NBRC 109396	GCA_000971235.1	1638989	1638989	type	True	80.3862	466	820	95	below_threshold
Demequina salsinemoris	strain=NBRC 105323	GCA_000974805.1	577470	577470	type	True	79.9905	394	820	95	below_threshold
Demequina globuliformis	strain=NBRC 106266	GCA_000975155.1	676202	676202	type	True	79.3446	374	820	95	below_threshold
Demequina flava	strain=NBRC 105854	GCA_000975035.1	1095025	1095025	type	True	79.0994	367	820	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.0529	294	820	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	77.9688	249	820	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	77.9014	281	820	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.8294	275	820	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	77.8237	264	820	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:11,029] [INFO] DFAST Taxonomy check result was written to GCF_016862815.1_ASM1686281v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:11,030] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:11,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:11,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/checkm_data
[2024-01-25 18:51:11,032] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:11,067] [INFO] Task started: CheckM
[2024-01-25 18:51:11,068] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862815.1_ASM1686281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862815.1_ASM1686281v1_genomic.fna/checkm_input GCF_016862815.1_ASM1686281v1_genomic.fna/checkm_result
[2024-01-25 18:51:52,656] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:52,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:52,674] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:52,674] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:52,675] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862815.1_ASM1686281v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:52,675] [INFO] Task started: Blastn
[2024-01-25 18:51:52,675] [INFO] Running command: blastn -query GCF_016862815.1_ASM1686281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47fbcbdd-7f00-4348-99e0-0812015221b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862815.1_ASM1686281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:54,519] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:54,522] [INFO] Selected 13 target genomes.
[2024-01-25 18:51:54,522] [INFO] Target genome list was writen to GCF_016862815.1_ASM1686281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:54,551] [INFO] Task started: fastANI
[2024-01-25 18:51:54,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd77aec-bac8-405f-979b-f1f8fe33a10e/GCF_016862815.1_ASM1686281v1_genomic.fna.gz --refList GCF_016862815.1_ASM1686281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862815.1_ASM1686281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:02,815] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:02,823] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:02,824] [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_016862815.1	s__Demequina activiva	100.0	820	820	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_002090155.1	s__Demequina sp002090155	82.726	608	820	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	82.2534	585	820	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	81.2574	562	820	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	80.9365	463	820	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	80.854	455	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.98	97.96	0.93	0.92	3	-
GCF_002090135.1	s__Demequina sp002090135	80.8147	476	820	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	80.7732	497	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971215.1	s__Demequina silvatica	80.7104	478	820	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	80.6439	479	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	97.20	96.53	0.93	0.91	3	-
GCF_000971395.1	s__Demequina iriomotensis	80.4296	453	820	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	80.3621	468	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002090075.1	s__Demequina sp002090075	80.1971	412	820	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Demequinaceae;g__Demequina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:02,825] [INFO] GTDB search result was written to GCF_016862815.1_ASM1686281v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:02,825] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:02,829] [INFO] DFAST_QC result json was written to GCF_016862815.1_ASM1686281v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:02,829] [INFO] DFAST_QC completed!
[2024-01-25 18:52:02,829] [INFO] Total running time: 0h1m12s