[2024-01-24 12:54:22,521] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,523] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference
[2024-01-24 12:54:23,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:23,972] [INFO] Task started: Prodigal
[2024-01-24 12:54:23,972] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3205c50-c117-47e4-b1b6-381be9be3700/GCF_000367525.1_ASM36752v2_genomic.fna.gz | prodigal -d GCF_000367525.1_ASM36752v2_genomic.fna/cds.fna -a GCF_000367525.1_ASM36752v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:34,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:34,055] [INFO] Task started: HMMsearch
[2024-01-24 12:54:34,055] [INFO] Running command: hmmsearch --tblout GCF_000367525.1_ASM36752v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/reference_markers.hmm GCF_000367525.1_ASM36752v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:34,318] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:34,320] [INFO] Found 6/6 markers.
[2024-01-24 12:54:34,354] [INFO] Query marker FASTA was written to GCF_000367525.1_ASM36752v2_genomic.fna/markers.fasta
[2024-01-24 12:54:34,354] [INFO] Task started: Blastn
[2024-01-24 12:54:34,354] [INFO] Running command: blastn -query GCF_000367525.1_ASM36752v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/reference_markers.fasta -out GCF_000367525.1_ASM36752v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:35,565] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:35,569] [INFO] Selected 20 target genomes.
[2024-01-24 12:54:35,569] [INFO] Target genome list was writen to GCF_000367525.1_ASM36752v2_genomic.fna/target_genomes.txt
[2024-01-24 12:54:35,576] [INFO] Task started: fastANI
[2024-01-24 12:54:35,577] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3205c50-c117-47e4-b1b6-381be9be3700/GCF_000367525.1_ASM36752v2_genomic.fna.gz --refList GCF_000367525.1_ASM36752v2_genomic.fna/target_genomes.txt --output GCF_000367525.1_ASM36752v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:48,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:48,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:48,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:48,756] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:48,756] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:48,757] [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
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	80.1247	456	1058	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	80.0858	470	1058	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	80.0854	510	1058	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.0459	515	1058	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.0008	507	1058	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.9368	517	1058	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.7534	474	1058	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	79.6535	447	1058	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	79.6114	473	1058	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.5507	412	1058	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.5412	459	1058	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.5336	371	1058	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.4222	439	1058	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.1009	374	1058	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.8222	321	1058	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.805	332	1058	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.6329	343	1058	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.5875	321	1058	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5789	331	1058	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.4283	336	1058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:48,759] [INFO] DFAST Taxonomy check result was written to GCF_000367525.1_ASM36752v2_genomic.fna/tc_result.tsv
[2024-01-24 12:54:48,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:48,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:48,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/checkm_data
[2024-01-24 12:54:48,761] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:48,798] [INFO] Task started: CheckM
[2024-01-24 12:54:48,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367525.1_ASM36752v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367525.1_ASM36752v2_genomic.fna/checkm_input GCF_000367525.1_ASM36752v2_genomic.fna/checkm_result
[2024-01-24 12:55:43,399] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:43,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:43,423] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:43,424] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:43,424] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367525.1_ASM36752v2_genomic.fna/markers.fasta)
[2024-01-24 12:55:43,425] [INFO] Task started: Blastn
[2024-01-24 12:55:43,425] [INFO] Running command: blastn -query GCF_000367525.1_ASM36752v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg458b43f2-c071-4eec-ad88-4e751ce4b9f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367525.1_ASM36752v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:45,160] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:45,165] [INFO] Selected 19 target genomes.
[2024-01-24 12:55:45,165] [INFO] Target genome list was writen to GCF_000367525.1_ASM36752v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:45,176] [INFO] Task started: fastANI
[2024-01-24 12:55:45,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3205c50-c117-47e4-b1b6-381be9be3700/GCF_000367525.1_ASM36752v2_genomic.fna.gz --refList GCF_000367525.1_ASM36752v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000367525.1_ASM36752v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:58,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:58,801] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:58,802] [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_000367525.1	s__Phycicoccus_A elongatus	100.0	1058	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus_A	95.0	98.36	98.36	0.88	0.88	2	conclusive
GCF_000720925.1	s__Phycicoccus jejuensis	80.1022	508	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_000768695.1	s__Knoellia aerolata	80.0998	458	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	80.0948	469	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	80.0438	502	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	80.0056	507	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017989115.1	s__Ornithinibacter sp017989115	79.9035	391	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	79.8891	521	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	79.7505	396	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	79.7356	529	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	79.6432	478	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846495.1	s__Phycicoccus duodecadis	79.6014	474	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104525.1	s__Pedococcus dokdonensis	79.5435	413	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	79.5182	461	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768705.1	s__Knoellia sinensis	79.4225	439	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716205.1	s__Oryzihumus leptocrescens	79.0896	379	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	79.0679	431	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715875.1	s__Terrabacter sp006715875	79.0063	405	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001247745.1	s__Luteipulveratus halotolerans	78.4121	338	1058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Luteipulveratus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:58,804] [INFO] GTDB search result was written to GCF_000367525.1_ASM36752v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:58,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:58,808] [INFO] DFAST_QC result json was written to GCF_000367525.1_ASM36752v2_genomic.fna/dqc_result.json
[2024-01-24 12:55:58,809] [INFO] DFAST_QC completed!
[2024-01-24 12:55:58,809] [INFO] Total running time: 0h1m36s