[2024-01-25 17:40:05,506] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:05,509] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:05,509] [INFO] DQC Reference Directory: /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference
[2024-01-25 17:40:06,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:06,671] [INFO] Task started: Prodigal
[2024-01-25 17:40:06,672] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e9e6e9e-0efe-447b-80f7-f1cf09d8cb44/GCF_003428165.1_ASM342816v1_genomic.fna.gz | prodigal -d GCF_003428165.1_ASM342816v1_genomic.fna/cds.fna -a GCF_003428165.1_ASM342816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:12,589] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:12,590] [INFO] Task started: HMMsearch
[2024-01-25 17:40:12,590] [INFO] Running command: hmmsearch --tblout GCF_003428165.1_ASM342816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/reference_markers.hmm GCF_003428165.1_ASM342816v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:12,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:12,824] [INFO] Found 6/6 markers.
[2024-01-25 17:40:12,851] [INFO] Query marker FASTA was written to GCF_003428165.1_ASM342816v1_genomic.fna/markers.fasta
[2024-01-25 17:40:12,851] [INFO] Task started: Blastn
[2024-01-25 17:40:12,851] [INFO] Running command: blastn -query GCF_003428165.1_ASM342816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/reference_markers.fasta -out GCF_003428165.1_ASM342816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:13,420] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:13,423] [INFO] Selected 23 target genomes.
[2024-01-25 17:40:13,424] [INFO] Target genome list was writen to GCF_003428165.1_ASM342816v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:13,435] [INFO] Task started: fastANI
[2024-01-25 17:40:13,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9e6e9e-0efe-447b-80f7-f1cf09d8cb44/GCF_003428165.1_ASM342816v1_genomic.fna.gz --refList GCF_003428165.1_ASM342816v1_genomic.fna/target_genomes.txt --output GCF_003428165.1_ASM342816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:26,620] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:26,621] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:26,621] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:26,628] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:40:26,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:26,628] [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
Cysteiniphilum litorale	strain=DSM 101832	GCA_003428165.1	2056700	2056700	type	True	100.0	988	993	95	conclusive
Cysteiniphilum litorale	strain=CGMCC 1.15758	GCA_014643575.1	2056700	2056700	type	True	99.9923	984	993	95	conclusive
Cysteiniphilum marinum	strain=19X3-30	GCA_014857925.1	2774191	2774191	type	True	90.6617	668	993	95	below_threshold
Cysteiniphilum halobium	strain=SYSU SYW-6	GCA_003574425.1	2219059	2219059	type	True	84.347	547	993	95	below_threshold
Fangia hongkongensis	strain=DSM 21703	GCA_000379445.1	270495	270495	type	True	78.1193	110	993	95	below_threshold
Fangia hongkongensis	strain=FSC776	GCA_016604485.1	270495	270495	type	True	78.1013	95	993	95	below_threshold
Caedibacter taeniospiralis	strain=51K	GCA_002803295.2	28907	28907	type	True	77.6993	132	993	95	below_threshold
Fastidiosibacter lacustris	strain=NBRC 112274	GCA_003428155.1	2056695	2056695	type	True	77.6532	153	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:26,629] [INFO] DFAST Taxonomy check result was written to GCF_003428165.1_ASM342816v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:26,630] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:26,631] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:26,631] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/checkm_data
[2024-01-25 17:40:26,631] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:26,665] [INFO] Task started: CheckM
[2024-01-25 17:40:26,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003428165.1_ASM342816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003428165.1_ASM342816v1_genomic.fna/checkm_input GCF_003428165.1_ASM342816v1_genomic.fna/checkm_result
[2024-01-25 17:40:49,418] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:49,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:49,443] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:49,443] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:49,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003428165.1_ASM342816v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:49,444] [INFO] Task started: Blastn
[2024-01-25 17:40:49,444] [INFO] Running command: blastn -query GCF_003428165.1_ASM342816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge47d4c64-598e-4419-b778-e866fc6171f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003428165.1_ASM342816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:50,237] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:50,240] [INFO] Selected 8 target genomes.
[2024-01-25 17:40:50,240] [INFO] Target genome list was writen to GCF_003428165.1_ASM342816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:50,251] [INFO] Task started: fastANI
[2024-01-25 17:40:50,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9e6e9e-0efe-447b-80f7-f1cf09d8cb44/GCF_003428165.1_ASM342816v1_genomic.fna.gz --refList GCF_003428165.1_ASM342816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003428165.1_ASM342816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:55,233] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:55,238] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:55,238] [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_003428165.1	s__Cysteiniphilum litorale	100.0	988	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.98	99.97	0.98	0.97	3	conclusive
GCF_008711525.1	s__Cysteiniphilum sp008711525	94.6771	627	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014857925.1	s__Cysteiniphilum marinum	90.6252	670	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	99.88	99.82	0.94	0.93	7	-
GCF_003574425.1	s__Cysteiniphilum halobium	84.3524	547	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Cysteiniphilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002803295.2	s__Caedibacter taeniospiralis	77.7085	131	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Caedibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428155.1	s__Fastidiosibacter lacustris	77.6532	153	993	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Francisellales;f__Francisellaceae;g__Fastidiosibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:55,239] [INFO] GTDB search result was written to GCF_003428165.1_ASM342816v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:55,240] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:55,242] [INFO] DFAST_QC result json was written to GCF_003428165.1_ASM342816v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:55,242] [INFO] DFAST_QC completed!
[2024-01-25 17:40:55,242] [INFO] Total running time: 0h0m50s