[2024-01-24 11:12:24,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,428] [INFO] DQC Reference Directory: /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference
[2024-01-24 11:12:27,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,093] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg00eccdd9-0f50-40a2-83e7-440999b8b1be/GCF_003351765.1_ASM335176v1_genomic.fna.gz | prodigal -d GCF_003351765.1_ASM335176v1_genomic.fna/cds.fna -a GCF_003351765.1_ASM335176v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:38,434] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:38,434] [INFO] Task started: HMMsearch
[2024-01-24 11:12:38,434] [INFO] Running command: hmmsearch --tblout GCF_003351765.1_ASM335176v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/reference_markers.hmm GCF_003351765.1_ASM335176v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:38,721] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:38,723] [INFO] Found 6/6 markers.
[2024-01-24 11:12:38,764] [INFO] Query marker FASTA was written to GCF_003351765.1_ASM335176v1_genomic.fna/markers.fasta
[2024-01-24 11:12:38,765] [INFO] Task started: Blastn
[2024-01-24 11:12:38,765] [INFO] Running command: blastn -query GCF_003351765.1_ASM335176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/reference_markers.fasta -out GCF_003351765.1_ASM335176v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:40,032] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:40,036] [INFO] Selected 13 target genomes.
[2024-01-24 11:12:40,036] [INFO] Target genome list was writen to GCF_003351765.1_ASM335176v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:40,055] [INFO] Task started: fastANI
[2024-01-24 11:12:40,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg00eccdd9-0f50-40a2-83e7-440999b8b1be/GCF_003351765.1_ASM335176v1_genomic.fna.gz --refList GCF_003351765.1_ASM335176v1_genomic.fna/target_genomes.txt --output GCF_003351765.1_ASM335176v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:51,641] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:51,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:51,642] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:51,653] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:51,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:51,653] [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 avium	strain=AMA3305	GCA_003351765.1	2283195	2283195	type	True	100.0	1306	1306	95	conclusive
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	83.3382	831	1306	95	below_threshold
Ornithinimicrobium pekingense	strain=CGMCC 1.5362	GCA_014644955.1	384677	384677	type	True	83.3096	820	1306	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	83.1294	759	1306	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	82.3775	737	1306	95	below_threshold
Ornithinimicrobium tianjinense	strain=CGMCC 1.12160	GCA_014636495.1	1195761	1195761	type	True	82.2457	736	1306	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	81.6481	741	1306	95	below_threshold
Ornithinimicrobium flavum	strain=CPCC 203535	GCA_004526345.1	1288636	1288636	type	True	81.6103	725	1306	95	below_threshold
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	81.3005	688	1306	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	81.0491	666	1306	95	below_threshold
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	80.7448	635	1306	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.8597	539	1306	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	79.3615	382	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:51,655] [INFO] DFAST Taxonomy check result was written to GCF_003351765.1_ASM335176v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:51,658] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:51,659] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:51,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/checkm_data
[2024-01-24 11:12:51,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:51,723] [INFO] Task started: CheckM
[2024-01-24 11:12:51,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003351765.1_ASM335176v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003351765.1_ASM335176v1_genomic.fna/checkm_input GCF_003351765.1_ASM335176v1_genomic.fna/checkm_result
[2024-01-24 11:13:51,305] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:51,307] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:51,330] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:51,330] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:51,331] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003351765.1_ASM335176v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:51,332] [INFO] Task started: Blastn
[2024-01-24 11:13:51,332] [INFO] Running command: blastn -query GCF_003351765.1_ASM335176v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19ab1ef9-ea27-400f-8055-6c2dfc611859/dqc_reference/reference_markers_gtdb.fasta -out GCF_003351765.1_ASM335176v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:53,321] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:53,325] [INFO] Selected 10 target genomes.
[2024-01-24 11:13:53,325] [INFO] Target genome list was writen to GCF_003351765.1_ASM335176v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:53,333] [INFO] Task started: fastANI
[2024-01-24 11:13:53,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg00eccdd9-0f50-40a2-83e7-440999b8b1be/GCF_003351765.1_ASM335176v1_genomic.fna.gz --refList GCF_003351765.1_ASM335176v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003351765.1_ASM335176v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:02,681] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:02,697] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:02,697] [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_003351765.1	s__Ornithinimicrobium sp003351765	100.0	1306	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003577095.1	s__Ornithinimicrobium sp003577095	87.338	697	1306	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	83.3239	832	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006716885.1	s__Ornithinimicrobium humiphilum	83.1117	758	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942405.1	s__Ornithinimicrobium sp001942405	82.5595	737	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	97.63	97.63	0.88	0.88	2	-
GCF_014636495.1	s__Ornithinimicrobium tianjinense	82.2346	737	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004322775.1	s__Serinicoccus sp004322775	81.7483	721	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003702705.1	s__Ornithinimicrobium cerasi	81.6517	741	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	96.64	96.64	0.85	0.85	2	-
GCF_004526345.1	s__Serinicoccus flavus	81.6377	722	1306	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	81.2853	689	1306	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:02,699] [INFO] GTDB search result was written to GCF_003351765.1_ASM335176v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:02,699] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:02,703] [INFO] DFAST_QC result json was written to GCF_003351765.1_ASM335176v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:02,704] [INFO] DFAST_QC completed!
[2024-01-24 11:14:02,704] [INFO] Total running time: 0h1m38s