[2024-01-25 19:05:35,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:35,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:35,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference
[2024-01-25 19:05:36,602] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:36,603] [INFO] Task started: Prodigal
[2024-01-25 19:05:36,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg0192ff01-7227-4517-b53e-933e7fb64f61/GCF_013409205.1_ASM1340920v1_genomic.fna.gz | prodigal -d GCF_013409205.1_ASM1340920v1_genomic.fna/cds.fna -a GCF_013409205.1_ASM1340920v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:45,535] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:45,535] [INFO] Task started: HMMsearch
[2024-01-25 19:05:45,535] [INFO] Running command: hmmsearch --tblout GCF_013409205.1_ASM1340920v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/reference_markers.hmm GCF_013409205.1_ASM1340920v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:45,763] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:45,764] [INFO] Found 6/6 markers.
[2024-01-25 19:05:45,793] [INFO] Query marker FASTA was written to GCF_013409205.1_ASM1340920v1_genomic.fna/markers.fasta
[2024-01-25 19:05:45,793] [INFO] Task started: Blastn
[2024-01-25 19:05:45,793] [INFO] Running command: blastn -query GCF_013409205.1_ASM1340920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/reference_markers.fasta -out GCF_013409205.1_ASM1340920v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:46,901] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:46,905] [INFO] Selected 13 target genomes.
[2024-01-25 19:05:46,906] [INFO] Target genome list was writen to GCF_013409205.1_ASM1340920v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:46,914] [INFO] Task started: fastANI
[2024-01-25 19:05:46,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg0192ff01-7227-4517-b53e-933e7fb64f61/GCF_013409205.1_ASM1340920v1_genomic.fna.gz --refList GCF_013409205.1_ASM1340920v1_genomic.fna/target_genomes.txt --output GCF_013409205.1_ASM1340920v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:56,474] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:56,474] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:56,475] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:56,483] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:05:56,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:56,483] [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
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	100.0	1102	1102	95	conclusive
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	83.2099	698	1102	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	83.1978	712	1102	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	83.0796	720	1102	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	83.024	700	1102	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	82.9914	674	1102	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	82.9751	682	1102	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	82.5242	702	1102	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	80.7643	528	1102	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	80.5839	581	1102	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.5804	345	1102	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.4393	343	1102	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.005	311	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:56,484] [INFO] DFAST Taxonomy check result was written to GCF_013409205.1_ASM1340920v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:56,485] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:56,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:56,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/checkm_data
[2024-01-25 19:05:56,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:56,518] [INFO] Task started: CheckM
[2024-01-25 19:05:56,518] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409205.1_ASM1340920v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409205.1_ASM1340920v1_genomic.fna/checkm_input GCF_013409205.1_ASM1340920v1_genomic.fna/checkm_result
[2024-01-25 19:06:55,895] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:55,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:55,914] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:55,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:55,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409205.1_ASM1340920v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:55,915] [INFO] Task started: Blastn
[2024-01-25 19:06:55,915] [INFO] Running command: blastn -query GCF_013409205.1_ASM1340920v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg272c2f56-bbe1-46e1-bb85-363305bc273d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409205.1_ASM1340920v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:57,687] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:57,690] [INFO] Selected 10 target genomes.
[2024-01-25 19:06:57,690] [INFO] Target genome list was writen to GCF_013409205.1_ASM1340920v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:57,715] [INFO] Task started: fastANI
[2024-01-25 19:06:57,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg0192ff01-7227-4517-b53e-933e7fb64f61/GCF_013409205.1_ASM1340920v1_genomic.fna.gz --refList GCF_013409205.1_ASM1340920v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409205.1_ASM1340920v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:05,408] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:05,415] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:05,415] [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_013409205.1	s__Janibacter cremeus	100.0	1102	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019116945.1	s__Janibacter merdipullorum	83.3788	652	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591405.1	s__Janibacter terrae	83.2102	710	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_001570945.1	s__Janibacter anophelis	83.2102	698	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_900176385.1	s__Janibacter indicus	83.068	721	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_004295485.1	s__Janibacter limosus_A	83.0321	754	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000297495.1	s__Janibacter hoylei	82.969	677	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001570985.1	s__Janibacter limosus	82.9569	683	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428305.1	s__Janibacter sp001428305	82.7498	758	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570965.1	s__Janibacter corallicola	82.5124	703	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:05,416] [INFO] GTDB search result was written to GCF_013409205.1_ASM1340920v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:05,417] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:05,421] [INFO] DFAST_QC result json was written to GCF_013409205.1_ASM1340920v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:05,421] [INFO] DFAST_QC completed!
[2024-01-25 19:07:05,421] [INFO] Total running time: 0h1m30s