[2024-01-24 13:27:45,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:45,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:45,196] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference
[2024-01-24 13:27:46,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:46,615] [INFO] Task started: Prodigal
[2024-01-24 13:27:46,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg9088b8f0-ba0e-460c-b92c-c7bdb6a1d3b5/GCF_008919445.1_ASM891944v1_genomic.fna.gz | prodigal -d GCF_008919445.1_ASM891944v1_genomic.fna/cds.fna -a GCF_008919445.1_ASM891944v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:57,332] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:57,333] [INFO] Task started: HMMsearch
[2024-01-24 13:27:57,333] [INFO] Running command: hmmsearch --tblout GCF_008919445.1_ASM891944v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/reference_markers.hmm GCF_008919445.1_ASM891944v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:57,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:57,673] [INFO] Found 6/6 markers.
[2024-01-24 13:27:57,720] [INFO] Query marker FASTA was written to GCF_008919445.1_ASM891944v1_genomic.fna/markers.fasta
[2024-01-24 13:27:57,721] [INFO] Task started: Blastn
[2024-01-24 13:27:57,721] [INFO] Running command: blastn -query GCF_008919445.1_ASM891944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/reference_markers.fasta -out GCF_008919445.1_ASM891944v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:58,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:58,928] [INFO] Selected 12 target genomes.
[2024-01-24 13:27:58,928] [INFO] Target genome list was writen to GCF_008919445.1_ASM891944v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:58,933] [INFO] Task started: fastANI
[2024-01-24 13:27:58,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg9088b8f0-ba0e-460c-b92c-c7bdb6a1d3b5/GCF_008919445.1_ASM891944v1_genomic.fna.gz --refList GCF_008919445.1_ASM891944v1_genomic.fna/target_genomes.txt --output GCF_008919445.1_ASM891944v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:08,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:08,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:08,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:08,856] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:08,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:08,857] [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
Serinicoccus kebangsaanensis	strain=P2D13-UKM	GCA_008919445.1	2602069	2602069	type	True	100.0	1147	1147	95	conclusive
Serinicoccus hydrothermalis	strain=JLT9	GCA_001685415.1	1758689	1758689	type	True	86.07	920	1147	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_008386315.1	247333	247333	type	True	85.3998	880	1147	95	below_threshold
Serinicoccus marinus	strain=DSM 15273	GCA_000421245.1	247333	247333	type	True	85.3804	870	1147	95	below_threshold
Serinicoccus chungangensis	strain=CCUG 59777	GCA_006337125.1	767452	767452	type	True	84.0699	848	1147	95	below_threshold
Serinicoccus sediminis	strain=GP-T3-3	GCA_004153545.1	2306021	2306021	type	True	83.9605	828	1147	95	below_threshold
Serinicoccus profundi	strain=MCCC 1A05965	GCA_000224715.2	1078471	1078471	type	True	83.9111	820	1147	95	below_threshold
Serinicoccus profundi	strain=CGMCC 4.5582	GCA_008001015.1	1078471	1078471	type	True	83.8959	855	1147	95	below_threshold
Ornithinimicrobium pekingense	strain=DSM 21552	GCA_000421185.1	384677	384677	type	True	81.148	663	1147	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	80.9268	633	1147	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	79.5556	507	1147	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.4195	332	1147	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:08,858] [INFO] DFAST Taxonomy check result was written to GCF_008919445.1_ASM891944v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:08,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:08,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:08,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/checkm_data
[2024-01-24 13:28:08,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:08,897] [INFO] Task started: CheckM
[2024-01-24 13:28:08,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008919445.1_ASM891944v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008919445.1_ASM891944v1_genomic.fna/checkm_input GCF_008919445.1_ASM891944v1_genomic.fna/checkm_result
[2024-01-24 13:29:04,904] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:04,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:04,928] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:04,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:04,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008919445.1_ASM891944v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:04,929] [INFO] Task started: Blastn
[2024-01-24 13:29:04,929] [INFO] Running command: blastn -query GCF_008919445.1_ASM891944v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a516e6a-02e6-4a99-b24e-244de21c2508/dqc_reference/reference_markers_gtdb.fasta -out GCF_008919445.1_ASM891944v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:06,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:06,846] [INFO] Selected 8 target genomes.
[2024-01-24 13:29:06,846] [INFO] Target genome list was writen to GCF_008919445.1_ASM891944v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:06,867] [INFO] Task started: fastANI
[2024-01-24 13:29:06,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg9088b8f0-ba0e-460c-b92c-c7bdb6a1d3b5/GCF_008919445.1_ASM891944v1_genomic.fna.gz --refList GCF_008919445.1_ASM891944v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008919445.1_ASM891944v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:14,630] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,644] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:14,644] [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_008919445.1	s__Serinicoccus sp008919445	100.0	1147	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001685415.1	s__Serinicoccus hydrothermalis	86.0606	922	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386315.1	s__Serinicoccus marinus	85.3873	881	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	98.28	97.42	0.92	0.87	4	-
GCF_006337125.1	s__Serinicoccus chungangensis	84.0806	847	1147	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	83.9892	870	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153545.1	s__Serinicoccus sediminis	83.9606	828	1147	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	83.9037	854	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Serinicoccus	95.0	99.17	98.35	0.97	0.94	3	-
GCF_000421185.1	s__Ornithinimicrobium pekingense	81.1711	661	1147	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,646] [INFO] GTDB search result was written to GCF_008919445.1_ASM891944v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:14,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:14,650] [INFO] DFAST_QC result json was written to GCF_008919445.1_ASM891944v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:14,650] [INFO] DFAST_QC completed!
[2024-01-24 13:29:14,650] [INFO] Total running time: 0h1m29s