[2023-06-29 20:13:52,810] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:13:52,813] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:13:52,813] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference
[2023-06-29 20:13:54,090] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:13:54,091] [INFO] Task started: Prodigal
[2023-06-29 20:13:54,092] [INFO] Running command: gunzip -c /var/lib/cwl/stgb961076d-c2a0-422e-b022-67e488dffcd2/GCA_021287075.1_ASM2128707v1_genomic.fna.gz | prodigal -d GCA_021287075.1_ASM2128707v1_genomic.fna/cds.fna -a GCA_021287075.1_ASM2128707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:14:04,588] [INFO] Task succeeded: Prodigal
[2023-06-29 20:14:04,588] [INFO] Task started: HMMsearch
[2023-06-29 20:14:04,588] [INFO] Running command: hmmsearch --tblout GCA_021287075.1_ASM2128707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/reference_markers.hmm GCA_021287075.1_ASM2128707v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:14:04,857] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:14:04,861] [INFO] Found 6/6 markers.
[2023-06-29 20:14:04,903] [INFO] Query marker FASTA was written to GCA_021287075.1_ASM2128707v1_genomic.fna/markers.fasta
[2023-06-29 20:14:04,904] [INFO] Task started: Blastn
[2023-06-29 20:14:04,904] [INFO] Running command: blastn -query GCA_021287075.1_ASM2128707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/reference_markers.fasta -out GCA_021287075.1_ASM2128707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:14:06,225] [INFO] Task succeeded: Blastn
[2023-06-29 20:14:06,230] [INFO] Selected 17 target genomes.
[2023-06-29 20:14:06,230] [INFO] Target genome list was writen to GCA_021287075.1_ASM2128707v1_genomic.fna/target_genomes.txt
[2023-06-29 20:14:06,232] [INFO] Task started: fastANI
[2023-06-29 20:14:06,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgb961076d-c2a0-422e-b022-67e488dffcd2/GCA_021287075.1_ASM2128707v1_genomic.fna.gz --refList GCA_021287075.1_ASM2128707v1_genomic.fna/target_genomes.txt --output GCA_021287075.1_ASM2128707v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:14:18,687] [INFO] Task succeeded: fastANI
[2023-06-29 20:14:18,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:14:18,688] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:14:18,701] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:14:18,701] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:14:18,702] [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 flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.2851	509	1167	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	80.2138	549	1167	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.1847	524	1167	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.9539	510	1167	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.9175	503	1167	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	79.8908	500	1167	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.836	475	1167	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.8088	523	1167	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.7805	507	1167	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	79.7272	463	1167	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.6214	427	1167	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.4279	418	1167	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.3999	486	1167	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.2928	429	1167	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	79.2501	476	1167	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	79.0224	426	1167	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	78.9361	403	1167	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:14:18,704] [INFO] DFAST Taxonomy check result was written to GCA_021287075.1_ASM2128707v1_genomic.fna/tc_result.tsv
[2023-06-29 20:14:18,704] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:14:18,704] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:14:18,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/checkm_data
[2023-06-29 20:14:18,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:14:18,741] [INFO] Task started: CheckM
[2023-06-29 20:14:18,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021287075.1_ASM2128707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021287075.1_ASM2128707v1_genomic.fna/checkm_input GCA_021287075.1_ASM2128707v1_genomic.fna/checkm_result
[2023-06-29 20:15:11,421] [INFO] Task succeeded: CheckM
[2023-06-29 20:15:11,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:15:11,446] [INFO] ===== Completeness check finished =====
[2023-06-29 20:15:11,446] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:15:11,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021287075.1_ASM2128707v1_genomic.fna/markers.fasta)
[2023-06-29 20:15:11,447] [INFO] Task started: Blastn
[2023-06-29 20:15:11,447] [INFO] Running command: blastn -query GCA_021287075.1_ASM2128707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc0ad371-1cf5-4c4f-8e32-9a3433f4abdc/dqc_reference/reference_markers_gtdb.fasta -out GCA_021287075.1_ASM2128707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:15:13,471] [INFO] Task succeeded: Blastn
[2023-06-29 20:15:13,477] [INFO] Selected 24 target genomes.
[2023-06-29 20:15:13,477] [INFO] Target genome list was writen to GCA_021287075.1_ASM2128707v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:15:13,486] [INFO] Task started: fastANI
[2023-06-29 20:15:13,486] [INFO] Running command: fastANI --query /var/lib/cwl/stgb961076d-c2a0-422e-b022-67e488dffcd2/GCA_021287075.1_ASM2128707v1_genomic.fna.gz --refList GCA_021287075.1_ASM2128707v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021287075.1_ASM2128707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:15:31,655] [INFO] Task succeeded: fastANI
[2023-06-29 20:15:31,675] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 20:15:31,675] [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_000768675.1	s__Knoellia flava	80.297	508	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111375.1	s__Pedococcus cremeus	80.2582	544	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	95.41	95.41	0.91	0.91	2	-
GCF_000720925.1	s__Phycicoccus jejuensis	79.9754	509	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_013041615.1	s__Pedococcus sp013041615	79.9564	516	1167	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	79.9337	503	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	79.9109	498	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	79.8757	523	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429605.1	s__Pedococcus sp001429605	79.8739	509	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCF_011383005.1	s__Phycicoccus sp011383005	79.7873	544	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	79.7546	540	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	79.7513	460	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_016887965.1	s__Phycicoccus sp016887965	79.6786	557	1167	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	79.6593	401	1167	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	79.6216	427	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006438965.1	s__Pedococcus bigeumensis	79.5109	494	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326735.1	s__Phycicoccus endophyticus	79.4504	475	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_004025965.2	s__Phycicoccus flavus	79.4117	484	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707125.1	s__Arsenicicoccus sp009707125	79.3984	421	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	79.3686	500	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	79.3546	512	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCF_000426385.1	s__Arsenicicoccus bolidensis	79.3164	470	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
GCF_006715875.1	s__Terrabacter sp006715875	79.2964	513	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189535.1	s__Arsenicicoccus sp001189535	79.2759	460	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570965.1	s__Janibacter corallicola	78.919	404	1167	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:15:31,677] [INFO] GTDB search result was written to GCA_021287075.1_ASM2128707v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:15:31,678] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:15:31,682] [INFO] DFAST_QC result json was written to GCA_021287075.1_ASM2128707v1_genomic.fna/dqc_result.json
[2023-06-29 20:15:31,683] [INFO] DFAST_QC completed!
[2023-06-29 20:15:31,683] [INFO] Total running time: 0h1m39s