[2024-01-25 19:45:35,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,438] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,438] [INFO] DQC Reference Directory: /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference
[2024-01-25 19:45:36,575] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:36,576] [INFO] Task started: Prodigal
[2024-01-25 19:45:36,579] [INFO] Running command: gunzip -c /var/lib/cwl/stge98bcd79-ae98-4775-96fd-46deb7018b70/GCF_009602535.1_ASM960253v1_genomic.fna.gz | prodigal -d GCF_009602535.1_ASM960253v1_genomic.fna/cds.fna -a GCF_009602535.1_ASM960253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:44,415] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:44,416] [INFO] Task started: HMMsearch
[2024-01-25 19:45:44,416] [INFO] Running command: hmmsearch --tblout GCF_009602535.1_ASM960253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/reference_markers.hmm GCF_009602535.1_ASM960253v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:44,623] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:44,624] [INFO] Found 6/6 markers.
[2024-01-25 19:45:44,650] [INFO] Query marker FASTA was written to GCF_009602535.1_ASM960253v1_genomic.fna/markers.fasta
[2024-01-25 19:45:44,650] [INFO] Task started: Blastn
[2024-01-25 19:45:44,650] [INFO] Running command: blastn -query GCF_009602535.1_ASM960253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/reference_markers.fasta -out GCF_009602535.1_ASM960253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:45,845] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:45,848] [INFO] Selected 22 target genomes.
[2024-01-25 19:45:45,848] [INFO] Target genome list was writen to GCF_009602535.1_ASM960253v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:45,862] [INFO] Task started: fastANI
[2024-01-25 19:45:45,862] [INFO] Running command: fastANI --query /var/lib/cwl/stge98bcd79-ae98-4775-96fd-46deb7018b70/GCF_009602535.1_ASM960253v1_genomic.fna.gz --refList GCF_009602535.1_ASM960253v1_genomic.fna/target_genomes.txt --output GCF_009602535.1_ASM960253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:59,823] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:59,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:59,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:59,836] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:45:59,837] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:59,837] [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
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	100.0	989	1000	95	conclusive
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	80.4368	479	1000	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	80.3649	512	1000	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	80.2455	477	1000	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	79.9384	451	1000	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	79.9143	445	1000	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	79.8715	466	1000	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	79.7918	509	1000	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	79.7493	469	1000	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	79.7332	504	1000	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	79.6928	456	1000	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	79.6899	436	1000	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	79.6829	452	1000	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	79.6496	444	1000	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	79.6279	429	1000	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	79.547	439	1000	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	79.4956	437	1000	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	79.2068	407	1000	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	79.2045	293	1000	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5769	278	1000	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	78.4802	325	1000	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	78.456	325	1000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:59,838] [INFO] DFAST Taxonomy check result was written to GCF_009602535.1_ASM960253v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:59,839] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:59,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:59,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/checkm_data
[2024-01-25 19:45:59,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:59,873] [INFO] Task started: CheckM
[2024-01-25 19:45:59,874] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009602535.1_ASM960253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009602535.1_ASM960253v1_genomic.fna/checkm_input GCF_009602535.1_ASM960253v1_genomic.fna/checkm_result
[2024-01-25 19:46:29,033] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:29,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:29,053] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:29,054] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:29,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009602535.1_ASM960253v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:29,055] [INFO] Task started: Blastn
[2024-01-25 19:46:29,055] [INFO] Running command: blastn -query GCF_009602535.1_ASM960253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg36967b8a-ca9c-440e-b93f-d0bfaa5fbbee/dqc_reference/reference_markers_gtdb.fasta -out GCF_009602535.1_ASM960253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:31,081] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:31,084] [INFO] Selected 22 target genomes.
[2024-01-25 19:46:31,084] [INFO] Target genome list was writen to GCF_009602535.1_ASM960253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:31,102] [INFO] Task started: fastANI
[2024-01-25 19:46:31,102] [INFO] Running command: fastANI --query /var/lib/cwl/stge98bcd79-ae98-4775-96fd-46deb7018b70/GCF_009602535.1_ASM960253v1_genomic.fna.gz --refList GCF_009602535.1_ASM960253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009602535.1_ASM960253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:46,863] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:46,877] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:46,877] [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_009602535.1	s__Ornithinicoccus_A halotolerans	100.0	989	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006716185.1	s__Ornithinicoccus hortensis	80.326	515	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	79.8778	448	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351765.1	s__Ornithinimicrobium sp003351765	79.8489	468	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	79.818	506	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003121625.1	s__Ornithinicoccus cavernae	79.745	469	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322775.1	s__Serinicoccus sp004322775	79.7245	453	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004153545.1	s__Serinicoccus sediminis	79.7174	453	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	79.7073	439	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685415.1	s__Serinicoccus hydrothermalis	79.676	453	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001483745.1	s__Serinicoccus chungangensis_A	79.6733	439	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	79.5637	438	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	79.5236	401	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004526345.1	s__Serinicoccus flavus	79.5147	435	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008919445.1	s__Serinicoccus sp008919445	79.4899	438	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577095.1	s__Ornithinimicrobium sp003577095	79.4555	390	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843165.1	s__Serinicoccus pratense	79.3641	422	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197575.1	s__Ornithinicoccus sp007197575	79.2163	407	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429605.1	s__Pedococcus sp001429605	78.4374	352	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCF_011326735.1	s__Phycicoccus endophyticus	78.4078	329	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_014646815.1	s__Terrabacter tumescens	78.0411	328	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001429185.1	s__Terrabacter sp001429185	77.8775	326	1000	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:46,878] [INFO] GTDB search result was written to GCF_009602535.1_ASM960253v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:46,879] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:46,883] [INFO] DFAST_QC result json was written to GCF_009602535.1_ASM960253v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:46,883] [INFO] DFAST_QC completed!
[2024-01-25 19:46:46,883] [INFO] Total running time: 0h1m11s