[2024-01-24 10:47:54,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference
[2024-01-24 10:48:03,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,344] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,344] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cf1b5eb-38a8-4e6f-b166-2a44173202c8/GCF_001591405.1_ASM159140v1_genomic.fna.gz | prodigal -d GCF_001591405.1_ASM159140v1_genomic.fna/cds.fna -a GCF_001591405.1_ASM159140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:13,486] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:13,486] [INFO] Task started: HMMsearch
[2024-01-24 10:48:13,487] [INFO] Running command: hmmsearch --tblout GCF_001591405.1_ASM159140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/reference_markers.hmm GCF_001591405.1_ASM159140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:13,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:13,763] [INFO] Found 6/6 markers.
[2024-01-24 10:48:13,796] [INFO] Query marker FASTA was written to GCF_001591405.1_ASM159140v1_genomic.fna/markers.fasta
[2024-01-24 10:48:13,796] [INFO] Task started: Blastn
[2024-01-24 10:48:13,797] [INFO] Running command: blastn -query GCF_001591405.1_ASM159140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/reference_markers.fasta -out GCF_001591405.1_ASM159140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:15,009] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:15,013] [INFO] Selected 13 target genomes.
[2024-01-24 10:48:15,013] [INFO] Target genome list was writen to GCF_001591405.1_ASM159140v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:15,024] [INFO] Task started: fastANI
[2024-01-24 10:48:15,025] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf1b5eb-38a8-4e6f-b166-2a44173202c8/GCF_001591405.1_ASM159140v1_genomic.fna.gz --refList GCF_001591405.1_ASM159140v1_genomic.fna/target_genomes.txt --output GCF_001591405.1_ASM159140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:25,650] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:25,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:25,665] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:25,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:25,666] [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 terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	100.0	1175	1186	95	conclusive
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	86.6614	854	1186	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	86.5339	819	1186	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	86.4687	794	1186	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	86.3865	788	1186	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	85.4251	809	1186	95	below_threshold
Janibacter cremeus	strain=DSM 26154	GCA_013409205.1	1285192	1285192	type	True	83.2256	712	1186	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	82.7794	640	1186	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	82.0853	697	1186	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	81.9733	633	1186	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.8385	417	1186	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.0363	362	1186	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.5931	240	1186	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,668] [INFO] DFAST Taxonomy check result was written to GCF_001591405.1_ASM159140v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:25,668] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:25,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:25,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/checkm_data
[2024-01-24 10:48:25,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:25,706] [INFO] Task started: CheckM
[2024-01-24 10:48:25,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591405.1_ASM159140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591405.1_ASM159140v1_genomic.fna/checkm_input GCF_001591405.1_ASM159140v1_genomic.fna/checkm_result
[2024-01-24 10:49:19,821] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:19,822] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:19,842] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:19,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:19,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591405.1_ASM159140v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:19,843] [INFO] Task started: Blastn
[2024-01-24 10:49:19,844] [INFO] Running command: blastn -query GCF_001591405.1_ASM159140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a0de929-e347-4913-89e1-111e96e3d3d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591405.1_ASM159140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:21,824] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:21,828] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:21,828] [INFO] Target genome list was writen to GCF_001591405.1_ASM159140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:21,836] [INFO] Task started: fastANI
[2024-01-24 10:49:21,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf1b5eb-38a8-4e6f-b166-2a44173202c8/GCF_001591405.1_ASM159140v1_genomic.fna.gz --refList GCF_001591405.1_ASM159140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591405.1_ASM159140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:30,739] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:30,754] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:30,755] [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_001591405.1	s__Janibacter terrae	100.0	1177	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	conclusive
GCF_900176385.1	s__Janibacter indicus	86.6615	854	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_001570945.1	s__Janibacter anophelis	86.5277	819	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_000297495.1	s__Janibacter hoylei	86.4283	786	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_004295485.1	s__Janibacter limosus_A	85.868	874	1186	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	85.428	862	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570985.1	s__Janibacter limosus	85.4121	810	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116945.1	s__Janibacter merdipullorum	84.491	688	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409205.1	s__Janibacter cremeus	83.224	713	1186	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	82.7912	639	1186	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:30,756] [INFO] GTDB search result was written to GCF_001591405.1_ASM159140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:30,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:30,760] [INFO] DFAST_QC result json was written to GCF_001591405.1_ASM159140v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:30,761] [INFO] DFAST_QC completed!
[2024-01-24 10:49:30,761] [INFO] Total running time: 0h1m37s