[2024-01-24 13:17:34,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,114] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,114] [INFO] DQC Reference Directory: /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference
[2024-01-24 13:17:35,498] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:35,499] [INFO] Task started: Prodigal
[2024-01-24 13:17:35,499] [INFO] Running command: gunzip -c /var/lib/cwl/stg13962389-cb3b-4d88-93a4-f72af16aa1f0/GCF_006716185.1_ASM671618v1_genomic.fna.gz | prodigal -d GCF_006716185.1_ASM671618v1_genomic.fna/cds.fna -a GCF_006716185.1_ASM671618v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:47,780] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:47,781] [INFO] Task started: HMMsearch
[2024-01-24 13:17:47,781] [INFO] Running command: hmmsearch --tblout GCF_006716185.1_ASM671618v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/reference_markers.hmm GCF_006716185.1_ASM671618v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:48,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:48,057] [INFO] Found 6/6 markers.
[2024-01-24 13:17:48,102] [INFO] Query marker FASTA was written to GCF_006716185.1_ASM671618v1_genomic.fna/markers.fasta
[2024-01-24 13:17:48,102] [INFO] Task started: Blastn
[2024-01-24 13:17:48,102] [INFO] Running command: blastn -query GCF_006716185.1_ASM671618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/reference_markers.fasta -out GCF_006716185.1_ASM671618v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:49,417] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:49,420] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:49,421] [INFO] Target genome list was writen to GCF_006716185.1_ASM671618v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:49,423] [INFO] Task started: fastANI
[2024-01-24 13:17:49,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg13962389-cb3b-4d88-93a4-f72af16aa1f0/GCF_006716185.1_ASM671618v1_genomic.fna.gz --refList GCF_006716185.1_ASM671618v1_genomic.fna/target_genomes.txt --output GCF_006716185.1_ASM671618v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:01,988] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:01,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:01,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,002] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:02,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:02,003] [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 hortensis	strain=DSM 12335	GCA_006716185.1	82346	82346	type	True	100.0	1310	1311	95	conclusive
Ornithinicoccus hortensis	strain=HKI0125	GCA_009602515.1	82346	82346	type	True	99.9028	1198	1311	95	conclusive
Ornithinimicrobium cavernae	strain=KCTC 49018	GCA_003121625.1	2666047	2666047	type	True	80.1488	694	1311	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	80.0293	627	1311	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	80.0132	446	1311	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.9854	547	1311	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	79.9407	567	1311	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	79.9389	517	1311	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	79.9091	525	1311	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	79.7234	524	1311	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	79.5363	519	1311	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	79.5225	525	1311	95	below_threshold
Serinicoccus profundi	strain=MCCC 1A05965	GCA_000224715.2	1078471	1078471	type	True	79.4485	486	1311	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	79.3942	513	1311	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	79.3578	535	1311	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5414	364	1311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,015] [INFO] DFAST Taxonomy check result was written to GCF_006716185.1_ASM671618v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,016] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/checkm_data
[2024-01-24 13:18:02,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,062] [INFO] Task started: CheckM
[2024-01-24 13:18:02,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716185.1_ASM671618v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716185.1_ASM671618v1_genomic.fna/checkm_input GCF_006716185.1_ASM671618v1_genomic.fna/checkm_result
[2024-01-24 13:18:49,185] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:49,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:49,206] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:49,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:49,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716185.1_ASM671618v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:49,207] [INFO] Task started: Blastn
[2024-01-24 13:18:49,208] [INFO] Running command: blastn -query GCF_006716185.1_ASM671618v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg375e85d7-7c43-4453-a761-ba7fad5dde0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716185.1_ASM671618v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:51,183] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:51,187] [INFO] Selected 19 target genomes.
[2024-01-24 13:18:51,187] [INFO] Target genome list was writen to GCF_006716185.1_ASM671618v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:51,218] [INFO] Task started: fastANI
[2024-01-24 13:18:51,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg13962389-cb3b-4d88-93a4-f72af16aa1f0/GCF_006716185.1_ASM671618v1_genomic.fna.gz --refList GCF_006716185.1_ASM671618v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716185.1_ASM671618v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:05,416] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:05,436] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:05,436] [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_006716185.1	s__Ornithinicoccus hortensis	100.0	1310	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009602535.1	s__Ornithinicoccus_A halotolerans	80.6076	518	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515595.1	s__Ornithinicoccus sp012515595	80.5532	559	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003121625.1	s__Ornithinicoccus cavernae	80.1492	694	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197575.1	s__Ornithinicoccus sp007197575	80.0067	630	1311	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	79.9875	448	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	79.9499	566	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	79.9461	522	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	79.877	529	1311	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	79.7348	522	1311	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	79.7285	448	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008919445.1	s__Serinicoccus sp008919445	79.5321	524	1311	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	79.5271	520	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006337125.1	s__Serinicoccus chungangensis	79.3896	531	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001015.1	s__Serinicoccus profundi	79.3404	516	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_004153545.1	s__Serinicoccus sediminis	79.3244	505	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003702705.1	s__Ornithinimicrobium cerasi	79.2263	520	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	-
GCF_006716205.1	s__Oryzihumus leptocrescens	78.9728	437	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Oryzihumus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002095.1	s__Allonocardiopsis opalescens	76.3591	390	1311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allonocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:05,438] [INFO] GTDB search result was written to GCF_006716185.1_ASM671618v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:05,438] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:05,442] [INFO] DFAST_QC result json was written to GCF_006716185.1_ASM671618v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:05,443] [INFO] DFAST_QC completed!
[2024-01-24 13:19:05,443] [INFO] Total running time: 0h1m31s