[2024-01-25 18:11:05,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:05,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:05,607] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference
[2024-01-25 18:11:06,784] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:06,785] [INFO] Task started: Prodigal
[2024-01-25 18:11:06,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd4b9141-6397-4f14-9cc5-311c3d5bf3cb/GCF_021272345.1_ASM2127234v1_genomic.fna.gz | prodigal -d GCF_021272345.1_ASM2127234v1_genomic.fna/cds.fna -a GCF_021272345.1_ASM2127234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:16,294] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:16,294] [INFO] Task started: HMMsearch
[2024-01-25 18:11:16,294] [INFO] Running command: hmmsearch --tblout GCF_021272345.1_ASM2127234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/reference_markers.hmm GCF_021272345.1_ASM2127234v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:16,515] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:16,516] [INFO] Found 6/6 markers.
[2024-01-25 18:11:16,547] [INFO] Query marker FASTA was written to GCF_021272345.1_ASM2127234v1_genomic.fna/markers.fasta
[2024-01-25 18:11:16,547] [INFO] Task started: Blastn
[2024-01-25 18:11:16,547] [INFO] Running command: blastn -query GCF_021272345.1_ASM2127234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/reference_markers.fasta -out GCF_021272345.1_ASM2127234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:17,730] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:17,733] [INFO] Selected 18 target genomes.
[2024-01-25 18:11:17,734] [INFO] Target genome list was writen to GCF_021272345.1_ASM2127234v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:17,755] [INFO] Task started: fastANI
[2024-01-25 18:11:17,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4b9141-6397-4f14-9cc5-311c3d5bf3cb/GCF_021272345.1_ASM2127234v1_genomic.fna.gz --refList GCF_021272345.1_ASM2127234v1_genomic.fna/target_genomes.txt --output GCF_021272345.1_ASM2127234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:11:30,985] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:30,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:11:30,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:11:30,996] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:11:30,996] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:11:30,997] [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
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	100.0	1166	1168	95	conclusive
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	80.1168	559	1168	95	below_threshold
Ornithinicoccus halotolerans	strain=EGI 80423	GCA_009602535.1	1748220	1748220	type	True	80.1015	493	1168	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	80.1014	551	1168	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	80.094	563	1168	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	79.9278	521	1168	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	79.8907	531	1168	95	below_threshold
Ornithinicoccus hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	79.8706	540	1168	95	below_threshold
Ornithinimicrobium avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	79.8249	546	1168	95	below_threshold
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	79.7957	539	1168	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	79.7949	517	1168	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	79.7948	503	1168	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	79.7608	522	1168	95	below_threshold
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	79.7315	521	1168	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	79.4094	483	1168	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	79.1729	363	1168	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.3872	343	1168	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	78.1808	385	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:11:30,999] [INFO] DFAST Taxonomy check result was written to GCF_021272345.1_ASM2127234v1_genomic.fna/tc_result.tsv
[2024-01-25 18:11:31,003] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:11:31,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:11:31,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/checkm_data
[2024-01-25 18:11:31,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:11:31,041] [INFO] Task started: CheckM
[2024-01-25 18:11:31,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021272345.1_ASM2127234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021272345.1_ASM2127234v1_genomic.fna/checkm_input GCF_021272345.1_ASM2127234v1_genomic.fna/checkm_result
[2024-01-25 18:12:32,830] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:32,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:32,857] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:32,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:32,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021272345.1_ASM2127234v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:32,859] [INFO] Task started: Blastn
[2024-01-25 18:12:32,859] [INFO] Running command: blastn -query GCF_021272345.1_ASM2127234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdc7524e-2afc-4c3e-9474-f901b21cb55c/dqc_reference/reference_markers_gtdb.fasta -out GCF_021272345.1_ASM2127234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:34,889] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:34,897] [INFO] Selected 18 target genomes.
[2024-01-25 18:12:34,897] [INFO] Target genome list was writen to GCF_021272345.1_ASM2127234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:34,911] [INFO] Task started: fastANI
[2024-01-25 18:12:34,911] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4b9141-6397-4f14-9cc5-311c3d5bf3cb/GCF_021272345.1_ASM2127234v1_genomic.fna.gz --refList GCF_021272345.1_ASM2127234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021272345.1_ASM2127234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:48,669] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:48,680] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:12:48,680] [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_000421185.1	s__Ornithinimicrobium pekingense	80.1063	560	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009602535.1	s__Ornithinicoccus_A halotolerans	80.0905	494	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	79.9712	516	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716185.1	s__Ornithinicoccus hortensis	79.901	537	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004153545.1	s__Serinicoccus sediminis	79.8813	532	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003351765.1	s__Ornithinimicrobium sp003351765	79.8696	541	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001685415.1	s__Serinicoccus hydrothermalis	79.8325	531	1168	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	79.8175	533	1168	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	79.7947	503	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386315.1	s__Serinicoccus marinus	79.7847	518	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	-
GCF_003702705.1	s__Ornithinimicrobium cerasi	79.7741	524	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	79.7634	441	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003577095.1	s__Ornithinimicrobium sp003577095	79.7533	405	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121625.1	s__Ornithinicoccus cavernae	79.7227	523	1168	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	79.6849	533	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322775.1	s__Serinicoccus sp004322775	79.6531	544	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007197575.1	s__Ornithinicoccus sp007197575	79.4557	478	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352835.1	s__Ornithinicoccus muralis	79.2013	361	1168	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:48,682] [INFO] GTDB search result was written to GCF_021272345.1_ASM2127234v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:48,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:48,686] [INFO] DFAST_QC result json was written to GCF_021272345.1_ASM2127234v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:48,686] [INFO] DFAST_QC completed!
[2024-01-25 18:12:48,686] [INFO] Total running time: 0h1m43s