[2024-01-25 18:45:35,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:35,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:35,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference
[2024-01-25 18:45:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:36,768] [INFO] Task started: Prodigal
[2024-01-25 18:45:36,768] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a1ed86e-d2c2-4b7f-b79c-179cf0e33572/GCF_028463985.1_ASM2846398v1_genomic.fna.gz | prodigal -d GCF_028463985.1_ASM2846398v1_genomic.fna/cds.fna -a GCF_028463985.1_ASM2846398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:42,430] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:42,430] [INFO] Task started: HMMsearch
[2024-01-25 18:45:42,430] [INFO] Running command: hmmsearch --tblout GCF_028463985.1_ASM2846398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/reference_markers.hmm GCF_028463985.1_ASM2846398v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:42,638] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:42,639] [INFO] Found 6/6 markers.
[2024-01-25 18:45:42,660] [INFO] Query marker FASTA was written to GCF_028463985.1_ASM2846398v1_genomic.fna/markers.fasta
[2024-01-25 18:45:42,660] [INFO] Task started: Blastn
[2024-01-25 18:45:42,660] [INFO] Running command: blastn -query GCF_028463985.1_ASM2846398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/reference_markers.fasta -out GCF_028463985.1_ASM2846398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:43,407] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:43,410] [INFO] Selected 20 target genomes.
[2024-01-25 18:45:43,410] [INFO] Target genome list was writen to GCF_028463985.1_ASM2846398v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:43,418] [INFO] Task started: fastANI
[2024-01-25 18:45:43,418] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1ed86e-d2c2-4b7f-b79c-179cf0e33572/GCF_028463985.1_ASM2846398v1_genomic.fna.gz --refList GCF_028463985.1_ASM2846398v1_genomic.fna/target_genomes.txt --output GCF_028463985.1_ASM2846398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:54,714] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:54,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:54,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:54,726] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:54,726] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:54,726] [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
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	80.6614	435	688	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	80.6413	340	688	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	80.4686	392	688	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	80.4452	387	688	95	below_threshold
Neisseria animalis	strain=DSM 23392	GCA_003795365.1	492	492	type	True	80.1708	390	688	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	80.0082	382	688	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	79.9622	393	688	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	79.8751	357	688	95	below_threshold
Neisseria meningitidis	strain=NCTC10025	GCA_900638555.1	487	487	type	True	79.8618	360	688	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	79.8446	351	688	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	79.8038	361	688	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	79.7753	382	688	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	79.7311	357	688	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	79.5121	387	688	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	79.4967	384	688	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	79.4915	309	688	95	below_threshold
Neisseria iguanae	strain=ATCC 51483	GCA_003013245.1	90242	90242	type	True	79.3972	344	688	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	79.3749	352	688	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	79.3447	376	688	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.1193	342	688	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:54,728] [INFO] DFAST Taxonomy check result was written to GCF_028463985.1_ASM2846398v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:54,729] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:54,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:54,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/checkm_data
[2024-01-25 18:45:54,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:54,753] [INFO] Task started: CheckM
[2024-01-25 18:45:54,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028463985.1_ASM2846398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028463985.1_ASM2846398v1_genomic.fna/checkm_input GCF_028463985.1_ASM2846398v1_genomic.fna/checkm_result
[2024-01-25 18:46:15,734] [INFO] Task succeeded: CheckM
[2024-01-25 18:46:15,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:46:15,747] [INFO] ===== Completeness check finished =====
[2024-01-25 18:46:15,748] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:46:15,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028463985.1_ASM2846398v1_genomic.fna/markers.fasta)
[2024-01-25 18:46:15,748] [INFO] Task started: Blastn
[2024-01-25 18:46:15,748] [INFO] Running command: blastn -query GCF_028463985.1_ASM2846398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg270d9dda-0455-454f-a011-84199f926613/dqc_reference/reference_markers_gtdb.fasta -out GCF_028463985.1_ASM2846398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:17,046] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:17,049] [INFO] Selected 24 target genomes.
[2024-01-25 18:46:17,049] [INFO] Target genome list was writen to GCF_028463985.1_ASM2846398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:46:17,059] [INFO] Task started: fastANI
[2024-01-25 18:46:17,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1ed86e-d2c2-4b7f-b79c-179cf0e33572/GCF_028463985.1_ASM2846398v1_genomic.fna.gz --refList GCF_028463985.1_ASM2846398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028463985.1_ASM2846398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:29,541] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:29,556] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:46:29,556] [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_014898075.1	s__Neisseria sp011038745	82.6302	414	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.25	98.87	0.98	0.97	4	-
GCF_001592185.1	s__Neisseria denitrificans	80.6276	341	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900636515.1	s__Neisseria animalis	80.4641	387	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_002216145.1	s__Neisseria chenwenguii	80.1919	422	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_013267835.1	s__Neisseria sp000186165	80.1048	357	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCA_001067655.1	s__Neisseria lactamica_B	80.0557	322	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_014054945.1	s__Neisseria sicca	79.9558	390	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_900638555.1	s__Neisseria meningitidis	79.9013	354	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	97.78	97.16	0.95	0.86	2138	-
GCF_001815675.1	s__Neisseria sp001815675	79.883	378	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4201	97.29	97.29	0.90	0.90	2	-
GCF_003044455.1	s__Neisseria bergeri	79.8446	342	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.18	96.14	0.94	0.92	5	-
GCF_003351665.1	s__Neisseria perflava	79.8299	360	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
GCF_005221285.1	s__Neisseria flavescens	79.8227	356	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_000260655.1	s__Neisseria sicca_B	79.8064	362	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_003315235.1	s__Neisseria gonorrhoeae	79.8018	330	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0389	99.56	98.98	0.97	0.89	796	-
GCF_001809325.1	s__Neisseria sp001809325	79.755	365	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_000227275.1	s__Neisseria sp000227275	79.7507	391	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_014055005.1	s__Neisseria dentiae	79.5315	380	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_001618085.1	s__Neisseria flavescens_C	79.5153	349	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003044645.1	s__Neisseria subflava_B	79.4356	350	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
GCF_003013245.1	s__Neisseria iguanae	79.3834	341	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187305.1	s__Neisseria zoodegmatis	79.1744	363	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_002108505.1	s__Neisseria dumasiana	79.1015	328	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_002237445.1	s__Neisseria sp002237445	78.9306	317	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_900636765.1	s__Neisseria canis	78.7464	247	688	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:29,558] [INFO] GTDB search result was written to GCF_028463985.1_ASM2846398v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:29,559] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:29,564] [INFO] DFAST_QC result json was written to GCF_028463985.1_ASM2846398v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:29,564] [INFO] DFAST_QC completed!
[2024-01-25 18:46:29,564] [INFO] Total running time: 0h0m54s