[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference
[2024-01-24 12:00:39,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,383] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,383] [INFO] Running command: gunzip -c /var/lib/cwl/stg1abae305-d741-4372-b613-34924d5faac2/GCF_006716205.1_ASM671620v1_genomic.fna.gz | prodigal -d GCF_006716205.1_ASM671620v1_genomic.fna/cds.fna -a GCF_006716205.1_ASM671620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:51,826] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:51,826] [INFO] Task started: HMMsearch
[2024-01-24 12:00:51,827] [INFO] Running command: hmmsearch --tblout GCF_006716205.1_ASM671620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/reference_markers.hmm GCF_006716205.1_ASM671620v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:52,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:52,113] [INFO] Found 6/6 markers.
[2024-01-24 12:00:52,158] [INFO] Query marker FASTA was written to GCF_006716205.1_ASM671620v1_genomic.fna/markers.fasta
[2024-01-24 12:00:52,159] [INFO] Task started: Blastn
[2024-01-24 12:00:52,159] [INFO] Running command: blastn -query GCF_006716205.1_ASM671620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/reference_markers.fasta -out GCF_006716205.1_ASM671620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:53,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:53,508] [INFO] Selected 21 target genomes.
[2024-01-24 12:00:53,509] [INFO] Target genome list was writen to GCF_006716205.1_ASM671620v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:53,518] [INFO] Task started: fastANI
[2024-01-24 12:00:53,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abae305-d741-4372-b613-34924d5faac2/GCF_006716205.1_ASM671620v1_genomic.fna.gz --refList GCF_006716205.1_ASM671620v1_genomic.fna/target_genomes.txt --output GCF_006716205.1_ASM671620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:08,642] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:08,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:08,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:08,662] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:01:08,662] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:01:08,662] [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
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	81.2234	697	1421	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	80.7839	611	1421	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	80.5197	574	1421	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	79.9858	535	1421	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.9504	531	1421	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.9274	524	1421	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	79.9051	544	1421	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	79.8828	542	1421	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	79.7602	516	1421	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.7278	465	1421	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.6712	485	1421	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	79.649	492	1421	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	79.4988	466	1421	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.4178	599	1421	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	79.4175	452	1421	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.2511	561	1421	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.0937	483	1421	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.9883	447	1421	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	78.9747	419	1421	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	78.8912	438	1421	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.332	402	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:08,665] [INFO] DFAST Taxonomy check result was written to GCF_006716205.1_ASM671620v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:08,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:08,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:08,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/checkm_data
[2024-01-24 12:01:08,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:08,710] [INFO] Task started: CheckM
[2024-01-24 12:01:08,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716205.1_ASM671620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716205.1_ASM671620v1_genomic.fna/checkm_input GCF_006716205.1_ASM671620v1_genomic.fna/checkm_result
[2024-01-24 12:02:30,598] [INFO] Task succeeded: CheckM
[2024-01-24 12:02:30,600] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:02:30,621] [INFO] ===== Completeness check finished =====
[2024-01-24 12:02:30,622] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:02:30,622] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716205.1_ASM671620v1_genomic.fna/markers.fasta)
[2024-01-24 12:02:30,623] [INFO] Task started: Blastn
[2024-01-24 12:02:30,623] [INFO] Running command: blastn -query GCF_006716205.1_ASM671620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c71f42e-82f3-49cf-909c-dac0949057f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716205.1_ASM671620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:02:32,746] [INFO] Task succeeded: Blastn
[2024-01-24 12:02:32,751] [INFO] Selected 21 target genomes.
[2024-01-24 12:02:32,751] [INFO] Target genome list was writen to GCF_006716205.1_ASM671620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:02:32,781] [INFO] Task started: fastANI
[2024-01-24 12:02:32,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abae305-d741-4372-b613-34924d5faac2/GCF_006716205.1_ASM671620v1_genomic.fna.gz --refList GCF_006716205.1_ASM671620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716205.1_ASM671620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:02:51,249] [INFO] Task succeeded: fastANI
[2024-01-24 12:02:51,271] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:02:51,271] [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_006716205.1	s__Oryzihumus leptocrescens	100.0	1419	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111375.1	s__Pedococcus cremeus	81.2918	694	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_001428025.1	s__Pedococcus sp001428025	80.8087	648	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	80.731	616	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426245.1	s__Pedococcus sp001426245	80.6278	656	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_013041615.1	s__Pedococcus sp013041615	80.4399	630	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009192725.1	s__Segeticoccus rhizosphaerae	80.2557	450	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Segeticoccus	95.0	99.13	99.13	0.90	0.90	2	-
GCF_014646815.1	s__Terrabacter tumescens	80.1002	609	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715875.1	s__Terrabacter sp006715875	79.9509	624	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	79.9379	523	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006715055.1	s__Lapillicoccus jejuensis	79.9085	625	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Lapillicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	79.8658	533	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707125.1	s__Arsenicicoccus sp009707125	79.6961	467	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383675.1	s__Terrabacter sp000383675	79.6296	617	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408565.1	s__Janibacter alkaliphilus	79.46	492	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002404345.1	s__UBA4719 sp002404345	79.3737	458	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377705.1	s__UBA4719 sp014377705	79.2912	455	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927555.1	s__UBA4719 sp012927555	79.2454	462	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	99.32	99.32	0.85	0.85	2	-
GCF_004025965.2	s__Phycicoccus flavus	79.2133	566	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132125.1	s__UBA4719 sp003132125	79.0488	368	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__UBA4719	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000719025.1	s__Kineosporia aurantiaca	77.4646	465	1421	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__Kineosporia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:02:51,273] [INFO] GTDB search result was written to GCF_006716205.1_ASM671620v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:02:51,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:02:51,279] [INFO] DFAST_QC result json was written to GCF_006716205.1_ASM671620v1_genomic.fna/dqc_result.json
[2024-01-24 12:02:51,279] [INFO] DFAST_QC completed!
[2024-01-24 12:02:51,279] [INFO] Total running time: 0h2m15s