[2024-01-24 13:10:19,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:10:19,559] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:10:19,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference
[2024-01-24 13:10:20,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:10:20,835] [INFO] Task started: Prodigal
[2024-01-24 13:10:20,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg6618782d-600a-4425-95e0-170130c92533/GCF_963394925.1_CCUG_346_T_genomic.fna.gz | prodigal -d GCF_963394925.1_CCUG_346_T_genomic.fna/cds.fna -a GCF_963394925.1_CCUG_346_T_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:26,691] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:26,691] [INFO] Task started: HMMsearch
[2024-01-24 13:10:26,691] [INFO] Running command: hmmsearch --tblout GCF_963394925.1_CCUG_346_T_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/reference_markers.hmm GCF_963394925.1_CCUG_346_T_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:26,956] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:26,958] [INFO] Found 6/6 markers.
[2024-01-24 13:10:26,984] [INFO] Query marker FASTA was written to GCF_963394925.1_CCUG_346_T_genomic.fna/markers.fasta
[2024-01-24 13:10:26,984] [INFO] Task started: Blastn
[2024-01-24 13:10:26,984] [INFO] Running command: blastn -query GCF_963394925.1_CCUG_346_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/reference_markers.fasta -out GCF_963394925.1_CCUG_346_T_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:27,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:27,775] [INFO] Selected 10 target genomes.
[2024-01-24 13:10:27,776] [INFO] Target genome list was writen to GCF_963394925.1_CCUG_346_T_genomic.fna/target_genomes.txt
[2024-01-24 13:10:27,781] [INFO] Task started: fastANI
[2024-01-24 13:10:27,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg6618782d-600a-4425-95e0-170130c92533/GCF_963394925.1_CCUG_346_T_genomic.fna.gz --refList GCF_963394925.1_CCUG_346_T_genomic.fna/target_genomes.txt --output GCF_963394925.1_CCUG_346_T_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:33,689] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:33,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:33,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:33,701] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:10:33,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:33,702] [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 cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	97.1049	563	650	95	conclusive
Neisseria cinerea	strain=FDAARGOS_871	GCA_016028715.1	483	483	type	True	97.072	563	650	95	conclusive
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	96.9262	567	650	95	conclusive
Neisseria cinerea	strain=ATCC 14685	GCA_000173895.1	483	483	type	True	96.9164	562	650	95	conclusive
Neisseria lactamica	strain=NCTC10617	GCA_901482445.1	486	486	type	True	90.2889	539	650	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	90.0978	545	650	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	86.5562	400	650	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	86.4352	424	650	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	85.7181	401	650	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	85.6095	379	650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:33,703] [INFO] DFAST Taxonomy check result was written to GCF_963394925.1_CCUG_346_T_genomic.fna/tc_result.tsv
[2024-01-24 13:10:33,704] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:33,704] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:33,704] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/checkm_data
[2024-01-24 13:10:33,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:33,739] [INFO] Task started: CheckM
[2024-01-24 13:10:33,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_963394925.1_CCUG_346_T_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_963394925.1_CCUG_346_T_genomic.fna/checkm_input GCF_963394925.1_CCUG_346_T_genomic.fna/checkm_result
[2024-01-24 13:10:58,207] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:58,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:58,229] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:58,229] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:58,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_963394925.1_CCUG_346_T_genomic.fna/markers.fasta)
[2024-01-24 13:10:58,230] [INFO] Task started: Blastn
[2024-01-24 13:10:58,230] [INFO] Running command: blastn -query GCF_963394925.1_CCUG_346_T_genomic.fna/markers.fasta -db /var/lib/cwl/stg2654d594-358e-48aa-8819-94d003287173/dqc_reference/reference_markers_gtdb.fasta -out GCF_963394925.1_CCUG_346_T_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:59,179] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:59,183] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:59,183] [INFO] Target genome list was writen to GCF_963394925.1_CCUG_346_T_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:59,195] [INFO] Task started: fastANI
[2024-01-24 13:10:59,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg6618782d-600a-4425-95e0-170130c92533/GCF_963394925.1_CCUG_346_T_genomic.fna.gz --refList GCF_963394925.1_CCUG_346_T_genomic.fna/target_genomes_gtdb.txt --output GCF_963394925.1_CCUG_346_T_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:05,537] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:05,548] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:05,548] [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_900475315.1	s__Neisseria cinerea	97.1211	563	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.50	96.82	0.94	0.93	8	conclusive
GCF_000176735.1	s__Neisseria polysaccharea	91.3648	514	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.23	95.40	0.91	0.88	7	-
GCF_003044455.1	s__Neisseria bergeri	91.1786	579	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_000193795.1	s__Neisseria lactamica_A	90.5387	539	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901482445.1	s__Neisseria lactamica	90.2696	540	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.73	97.33	0.93	0.89	36	-
GCF_900638555.1	s__Neisseria meningitidis	90.0937	546	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	97.78	97.16	0.95	0.86	2138	-
GCF_003315235.1	s__Neisseria gonorrhoeae	89.5633	518	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	99.56	98.98	0.97	0.89	796	-
GCF_001618085.1	s__Neisseria flavescens_C	85.9053	390	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003045025.1	s__Neisseria subflava_A	85.3988	398	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
GCF_013267835.1	s__Neisseria sp000186165	85.3887	378	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_900654165.1	s__Neisseria subflava_C	85.2992	385	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.16	95.72	0.94	0.90	27	-
GCF_003044645.1	s__Neisseria subflava_B	85.1425	392	650	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:05,550] [INFO] GTDB search result was written to GCF_963394925.1_CCUG_346_T_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:05,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:05,554] [INFO] DFAST_QC result json was written to GCF_963394925.1_CCUG_346_T_genomic.fna/dqc_result.json
[2024-01-24 13:11:05,554] [INFO] DFAST_QC completed!
[2024-01-24 13:11:05,554] [INFO] Total running time: 0h0m46s