[2024-01-24 13:57:44,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:44,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:44,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference
[2024-01-24 13:57:46,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:46,385] [INFO] Task started: Prodigal
[2024-01-24 13:57:46,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg55d50849-9c60-4b5e-99c6-6504d61017ff/GCF_001570985.1_ASM157098v1_genomic.fna.gz | prodigal -d GCF_001570985.1_ASM157098v1_genomic.fna/cds.fna -a GCF_001570985.1_ASM157098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,381] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,382] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,382] [INFO] Running command: hmmsearch --tblout GCF_001570985.1_ASM157098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/reference_markers.hmm GCF_001570985.1_ASM157098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,662] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,693] [INFO] Query marker FASTA was written to GCF_001570985.1_ASM157098v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,693] [INFO] Task started: Blastn
[2024-01-24 13:57:56,693] [INFO] Running command: blastn -query GCF_001570985.1_ASM157098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/reference_markers.fasta -out GCF_001570985.1_ASM157098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,843] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:57,844] [INFO] Target genome list was writen to GCF_001570985.1_ASM157098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,849] [INFO] Task started: fastANI
[2024-01-24 13:57:57,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d50849-9c60-4b5e-99c6-6504d61017ff/GCF_001570985.1_ASM157098v1_genomic.fna.gz --refList GCF_001570985.1_ASM157098v1_genomic.fna/target_genomes.txt --output GCF_001570985.1_ASM157098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:08,481] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:08,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:08,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:08,495] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:08,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:08,496] [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 limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	100.0	1074	1078	95	conclusive
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	86.0417	828	1078	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	85.3973	784	1078	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	85.3562	813	1078	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	85.2986	799	1078	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	85.2154	795	1078	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	82.0356	640	1078	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	81.0243	593	1078	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	80.9745	568	1078	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.6207	349	1078	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.5994	336	1078	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.398	371	1078	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.3804	385	1078	95	below_threshold
Ornithinimicrobium murale	strain=DSM 22056	GCA_003352835.1	1050153	1050153	type	True	77.6002	197	1078	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,497] [INFO] DFAST Taxonomy check result was written to GCF_001570985.1_ASM157098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:08,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:08,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:08,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/checkm_data
[2024-01-24 13:58:08,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:08,543] [INFO] Task started: CheckM
[2024-01-24 13:58:08,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001570985.1_ASM157098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001570985.1_ASM157098v1_genomic.fna/checkm_input GCF_001570985.1_ASM157098v1_genomic.fna/checkm_result
[2024-01-24 13:59:03,200] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:03,201] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:03,223] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:03,223] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:03,224] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001570985.1_ASM157098v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:03,224] [INFO] Task started: Blastn
[2024-01-24 13:59:03,224] [INFO] Running command: blastn -query GCF_001570985.1_ASM157098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg292c842c-78f1-4212-831a-6741d8fc7f6e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001570985.1_ASM157098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:05,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:05,006] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:05,006] [INFO] Target genome list was writen to GCF_001570985.1_ASM157098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:05,013] [INFO] Task started: fastANI
[2024-01-24 13:59:05,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg55d50849-9c60-4b5e-99c6-6504d61017ff/GCF_001570985.1_ASM157098v1_genomic.fna.gz --refList GCF_001570985.1_ASM157098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001570985.1_ASM157098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:11,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:11,558] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:11,558] [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_001570985.1	s__Janibacter limosus	100.0	1074	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001428305.1	s__Janibacter sp001428305	89.8025	930	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295485.1	s__Janibacter limosus_A	89.4891	906	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570945.1	s__Janibacter anophelis	86.0168	830	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_001591405.1	s__Janibacter terrae	85.3562	813	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_900176385.1	s__Janibacter indicus	85.2987	799	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	-
GCF_000297495.1	s__Janibacter hoylei	85.2317	794	1078	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCA_019116945.1	s__Janibacter merdipullorum	83.6172	690	1078	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 13:59:11,560] [INFO] GTDB search result was written to GCF_001570985.1_ASM157098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:11,560] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:11,564] [INFO] DFAST_QC result json was written to GCF_001570985.1_ASM157098v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:11,564] [INFO] DFAST_QC completed!
[2024-01-24 13:59:11,564] [INFO] Total running time: 0h1m27s