[2024-01-24 13:55:27,687] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:27,692] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:27,693] [INFO] DQC Reference Directory: /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference
[2024-01-24 13:55:28,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:28,930] [INFO] Task started: Prodigal
[2024-01-24 13:55:28,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg373ed4bd-200d-4d50-b8fd-af35828b7fcf/GCF_963396225.1_CCUG_23930_T_genomic.fna.gz | prodigal -d GCF_963396225.1_CCUG_23930_T_genomic.fna/cds.fna -a GCF_963396225.1_CCUG_23930_T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:35,128] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:35,128] [INFO] Task started: HMMsearch
[2024-01-24 13:55:35,128] [INFO] Running command: hmmsearch --tblout GCF_963396225.1_CCUG_23930_T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/reference_markers.hmm GCF_963396225.1_CCUG_23930_T_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:35,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:35,348] [INFO] Found 6/6 markers.
[2024-01-24 13:55:35,370] [INFO] Query marker FASTA was written to GCF_963396225.1_CCUG_23930_T_genomic.fna/markers.fasta
[2024-01-24 13:55:35,370] [INFO] Task started: Blastn
[2024-01-24 13:55:35,370] [INFO] Running command: blastn -query GCF_963396225.1_CCUG_23930_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/reference_markers.fasta -out GCF_963396225.1_CCUG_23930_T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:36,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:36,065] [INFO] Selected 11 target genomes.
[2024-01-24 13:55:36,065] [INFO] Target genome list was writen to GCF_963396225.1_CCUG_23930_T_genomic.fna/target_genomes.txt
[2024-01-24 13:55:36,076] [INFO] Task started: fastANI
[2024-01-24 13:55:36,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg373ed4bd-200d-4d50-b8fd-af35828b7fcf/GCF_963396225.1_CCUG_23930_T_genomic.fna.gz --refList GCF_963396225.1_CCUG_23930_T_genomic.fna/target_genomes.txt --output GCF_963396225.1_CCUG_23930_T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:43,605] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:43,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:43,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:43,615] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:43,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:43,616] [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
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	99.9969	693	693	95	conclusive
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	94.7951	604	693	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	94.7491	613	693	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	94.4559	605	693	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	85.8374	373	693	95	below_threshold
Neisseria cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	85.7608	373	693	95	below_threshold
Neisseria cinerea	strain=ATCC 14685	GCA_000173895.1	483	483	type	True	85.6115	373	693	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	84.8941	465	693	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	84.8713	492	693	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	84.6113	506	693	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	84.4279	406	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:43,617] [INFO] DFAST Taxonomy check result was written to GCF_963396225.1_CCUG_23930_T_genomic.fna/tc_result.tsv
[2024-01-24 13:55:43,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:43,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:43,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/checkm_data
[2024-01-24 13:55:43,619] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:43,641] [INFO] Task started: CheckM
[2024-01-24 13:55:43,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_963396225.1_CCUG_23930_T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_963396225.1_CCUG_23930_T_genomic.fna/checkm_input GCF_963396225.1_CCUG_23930_T_genomic.fna/checkm_result
[2024-01-24 13:56:06,762] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:06,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:06,779] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:06,779] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:06,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_963396225.1_CCUG_23930_T_genomic.fna/markers.fasta)
[2024-01-24 13:56:06,780] [INFO] Task started: Blastn
[2024-01-24 13:56:06,780] [INFO] Running command: blastn -query GCF_963396225.1_CCUG_23930_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg2566eee5-a2e2-4b25-ae66-8655a95db5dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_963396225.1_CCUG_23930_T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:07,924] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:07,927] [INFO] Selected 10 target genomes.
[2024-01-24 13:56:07,928] [INFO] Target genome list was writen to GCF_963396225.1_CCUG_23930_T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:07,940] [INFO] Task started: fastANI
[2024-01-24 13:56:07,940] [INFO] Running command: fastANI --query /var/lib/cwl/stg373ed4bd-200d-4d50-b8fd-af35828b7fcf/GCF_963396225.1_CCUG_23930_T_genomic.fna.gz --refList GCF_963396225.1_CCUG_23930_T_genomic.fna/target_genomes_gtdb.txt --output GCF_963396225.1_CCUG_23930_T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:14,319] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:14,328] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:14,328] [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_005221305.1	s__Neisseria subflava	99.9969	693	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	96.50	96.31	0.91	0.87	10	conclusive
GCF_001618015.1	s__Neisseria flavescens_B	95.1123	620	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.1594	95.75	95.73	0.88	0.87	5	-
GCF_005221285.1	s__Neisseria flavescens	94.7951	604	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_003045025.1	s__Neisseria subflava_A	94.6502	635	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
GCF_001618085.1	s__Neisseria flavescens_C	94.607	615	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_001618065.1	s__Neisseria flavescens_A	94.5934	613	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6469	95.75	95.69	0.92	0.91	4	-
GCF_003044645.1	s__Neisseria subflava_B	94.5882	618	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
GCF_003351665.1	s__Neisseria perflava	94.5183	631	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
GCF_900654165.1	s__Neisseria subflava_C	94.4861	639	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.16	95.72	0.94	0.90	27	-
GCF_013267835.1	s__Neisseria sp000186165	93.7458	630	693	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:14,329] [INFO] GTDB search result was written to GCF_963396225.1_CCUG_23930_T_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:14,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:14,333] [INFO] DFAST_QC result json was written to GCF_963396225.1_CCUG_23930_T_genomic.fna/dqc_result.json
[2024-01-24 13:56:14,333] [INFO] DFAST_QC completed!
[2024-01-24 13:56:14,333] [INFO] Total running time: 0h0m47s