[2024-01-24 13:28:29,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,107] [INFO] DQC Reference Directory: /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference
[2024-01-24 13:28:30,313] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,314] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg30f5671c-459f-4c02-aca0-7b75d17e0384/GCF_022749515.1_ASM2274951v1_genomic.fna.gz | prodigal -d GCF_022749515.1_ASM2274951v1_genomic.fna/cds.fna -a GCF_022749515.1_ASM2274951v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:37,921] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:37,921] [INFO] Task started: HMMsearch
[2024-01-24 13:28:37,922] [INFO] Running command: hmmsearch --tblout GCF_022749515.1_ASM2274951v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/reference_markers.hmm GCF_022749515.1_ASM2274951v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:38,197] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:38,199] [INFO] Found 6/6 markers.
[2024-01-24 13:28:38,224] [INFO] Query marker FASTA was written to GCF_022749515.1_ASM2274951v1_genomic.fna/markers.fasta
[2024-01-24 13:28:38,225] [INFO] Task started: Blastn
[2024-01-24 13:28:38,225] [INFO] Running command: blastn -query GCF_022749515.1_ASM2274951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/reference_markers.fasta -out GCF_022749515.1_ASM2274951v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:38,994] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:38,998] [INFO] Selected 12 target genomes.
[2024-01-24 13:28:38,998] [INFO] Target genome list was writen to GCF_022749515.1_ASM2274951v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:39,007] [INFO] Task started: fastANI
[2024-01-24 13:28:39,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f5671c-459f-4c02-aca0-7b75d17e0384/GCF_022749515.1_ASM2274951v1_genomic.fna.gz --refList GCF_022749515.1_ASM2274951v1_genomic.fna/target_genomes.txt --output GCF_022749515.1_ASM2274951v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:05,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:05,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:05,667] [WARNING] Following organisms are indistinguishable with ANI. [Morococcus cerebrosus(1056807), Neisseria mucosa(488), Neisseria sicca(490)]
[2024-01-24 13:29:05,668] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:29:05,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:05,668] [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
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	100.0	855	858	95	conclusive
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	99.8376	728	858	95	conclusive
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	93.767	635	858	95	below_threshold
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	93.7476	654	858	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	86.4763	413	858	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	85.6793	456	858	95	below_threshold
Neisseria subflava	strain=ATCC 49275	GCA_005221305.1	28449	28449	type	True	85.2883	477	858	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	84.9325	359	858	95	below_threshold
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	84.8271	366	858	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	84.7636	362	858	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	84.7575	486	858	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	83.8259	464	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,670] [INFO] DFAST Taxonomy check result was written to GCF_022749515.1_ASM2274951v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:05,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:05,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:05,671] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/checkm_data
[2024-01-24 13:29:05,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:05,700] [INFO] Task started: CheckM
[2024-01-24 13:29:05,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022749515.1_ASM2274951v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022749515.1_ASM2274951v1_genomic.fna/checkm_input GCF_022749515.1_ASM2274951v1_genomic.fna/checkm_result
[2024-01-24 13:29:33,084] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:33,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:33,105] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:33,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:33,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022749515.1_ASM2274951v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:33,106] [INFO] Task started: Blastn
[2024-01-24 13:29:33,106] [INFO] Running command: blastn -query GCF_022749515.1_ASM2274951v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2659f0a-b3d8-4a0b-aa89-15edb68a075d/dqc_reference/reference_markers_gtdb.fasta -out GCF_022749515.1_ASM2274951v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:34,492] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:34,495] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:34,495] [INFO] Target genome list was writen to GCF_022749515.1_ASM2274951v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:34,503] [INFO] Task started: fastANI
[2024-01-24 13:29:34,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f5671c-459f-4c02-aca0-7b75d17e0384/GCF_022749515.1_ASM2274951v1_genomic.fna.gz --refList GCF_022749515.1_ASM2274951v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022749515.1_ASM2274951v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:02,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:02,737] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:02,737] [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_000813705.1	s__Neisseria cerebrosa	99.8376	728	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	97.92	97.52	0.91	0.89	5	conclusive
GCA_003028315.1	s__Neisseria mucosa	96.4095	738	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	96.97	96.70	0.92	0.90	9	-
GCF_000952795.1	s__Neisseria sp000952795	95.8823	689	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4916	98.25	96.69	0.90	0.83	3	-
GCF_003044425.1	s__Neisseria sicca_C	95.6848	678	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.8064	96.78	96.77	0.93	0.92	3	-
GCF_017753665.1	s__Neisseria sicca_D	95.0577	710	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_000193735.1	s__Neisseria sicca_E	94.2045	656	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260655.1	s__Neisseria sicca_B	93.7849	587	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_000227275.1	s__Neisseria sp000227275	93.7408	639	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_014054945.1	s__Neisseria sicca	93.6852	656	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCA_000220865.1	s__Neisseria macacae	93.6548	638	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCA_001067655.1	s__Neisseria lactamica_B	92.8874	533	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_005886145.1	s__Neisseria sp000090875	87.8636	492	858	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:02,738] [INFO] GTDB search result was written to GCF_022749515.1_ASM2274951v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:02,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:02,742] [INFO] DFAST_QC result json was written to GCF_022749515.1_ASM2274951v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:02,743] [INFO] DFAST_QC completed!
[2024-01-24 13:30:02,743] [INFO] Total running time: 0h1m34s