[2024-01-24 13:09:49,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:49,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:49,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference
[2024-01-24 13:09:50,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:50,622] [INFO] Task started: Prodigal
[2024-01-24 13:09:50,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f1fcb02-3b3a-401f-9590-ae9f1edccb0d/GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/cds.fna -a GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:57,614] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:57,615] [INFO] Task started: HMMsearch
[2024-01-24 13:09:57,615] [INFO] Running command: hmmsearch --tblout GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/reference_markers.hmm GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:57,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:57,901] [INFO] Found 6/6 markers.
[2024-01-24 13:09:57,927] [INFO] Query marker FASTA was written to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:57,928] [INFO] Task started: Blastn
[2024-01-24 13:09:57,928] [INFO] Running command: blastn -query GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/reference_markers.fasta -out GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:58,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:58,679] [INFO] Selected 13 target genomes.
[2024-01-24 13:09:58,679] [INFO] Target genome list was writen to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:58,714] [INFO] Task started: fastANI
[2024-01-24 13:09:58,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f1fcb02-3b3a-401f-9590-ae9f1edccb0d/GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna.gz --refList GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:10,622] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:10,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:10,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:10,634] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:10:10,634] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:10,634] [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 elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	100.0	773	775	95	conclusive
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	99.9957	774	775	95	conclusive
Neisseria elongata subsp. glycolytica	strain=ATCC 29315	GCA_000818035.1	88719	495	type	True	96.1039	676	775	95	conclusive
Neisseria elongata subsp. glycolytica	strain=NCTC11050	GCA_900475815.1	88719	495	type	True	96.0764	671	775	95	conclusive
Neisseria sicca	strain=DSM 17713	GCA_014054945.1	490	490	suspected-type	True	84.8712	402	775	95	below_threshold
Neisseria sicca	strain=ATCC 29256	GCA_000174655.1	490	490	suspected-type	True	84.8466	391	775	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_000813705.1	1056807	1056807	type	True	84.3697	371	775	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	84.1554	399	775	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	82.9973	311	775	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	82.6377	331	775	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	81.5349	321	775	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	81.3688	474	775	95	below_threshold
Neisseria canis	strain=ATCC 14687	GCA_002108495.1	493	493	type	True	78.722	270	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:10,636] [INFO] DFAST Taxonomy check result was written to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:10:10,636] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:10,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:10,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/checkm_data
[2024-01-24 13:10:10,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:10,663] [INFO] Task started: CheckM
[2024-01-24 13:10:10,663] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/checkm_input GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:36,418] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:36,420] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.72%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:36,440] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:36,440] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:36,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:36,441] [INFO] Task started: Blastn
[2024-01-24 13:10:36,441] [INFO] Running command: blastn -query GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg35633158-ba7b-49f6-8333-3b93af334e1e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:37,769] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:37,772] [INFO] Selected 22 target genomes.
[2024-01-24 13:10:37,773] [INFO] Target genome list was writen to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:37,874] [INFO] Task started: fastANI
[2024-01-24 13:10:37,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f1fcb02-3b3a-401f-9590-ae9f1edccb0d/GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna.gz --refList GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:52,983] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:53,011] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:53,011] [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_900113545.1	s__Neisseria elongata	100.0	773	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	conclusive
GCF_003044565.1	s__Neisseria sicca_A	84.9144	389	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.01	95.27	0.94	0.92	3	-
GCA_001067655.1	s__Neisseria lactamica_B	84.8771	338	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCF_001809325.1	s__Neisseria sp001809325	84.8562	373	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.406	N/A	N/A	N/A	N/A	1	-
GCA_000220865.1	s__Neisseria macacae	84.7664	390	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
GCF_014054945.1	s__Neisseria sicca	84.7522	407	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_000227275.1	s__Neisseria sp000227275	84.7495	398	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.3387	97.52	96.71	0.95	0.93	3	-
GCF_000260655.1	s__Neisseria sicca_B	84.6951	377	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_017753665.1	s__Neisseria sicca_D	84.6388	382	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.2415	96.44	95.35	0.92	0.88	6	-
GCF_003044425.1	s__Neisseria sicca_C	84.6296	369	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.8064	96.78	96.77	0.93	0.92	3	-
GCF_000952795.1	s__Neisseria sp000952795	84.5344	356	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4916	98.25	96.69	0.90	0.83	3	-
GCF_000813705.1	s__Neisseria cerebrosa	84.3902	370	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	97.92	97.52	0.91	0.89	5	-
GCA_003028315.1	s__Neisseria mucosa	84.3865	386	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5429	96.97	96.70	0.92	0.90	9	-
GCF_005886145.1	s__Neisseria sp000090875	84.1834	387	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_901482445.1	s__Neisseria lactamica	82.9696	341	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.73	97.33	0.93	0.89	36	-
GCF_002237445.1	s__Neisseria sp002237445	81.8202	495	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_014055025.1	s__Neisseria bacilliformis	81.441	466	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_900637855.1	s__Neisseria animaloris	78.7695	301	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_900636765.1	s__Neisseria canis	78.7558	274	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000227765.1	s__Neisseria wadsworthii	78.4832	246	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.36	97.06	0.97	0.96	3	-
GCF_001308015.1	s__Neisseria sp001308015	78.4269	233	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002951835.1	s__Simonsiella muelleri	77.3341	65	775	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Simonsiella	95.0	99.93	99.93	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:53,013] [INFO] GTDB search result was written to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:53,014] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:53,018] [INFO] DFAST_QC result json was written to GCF_900113545.1_IMG-taxon_2675903696_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:10:53,018] [INFO] DFAST_QC completed!
[2024-01-24 13:10:53,018] [INFO] Total running time: 0h1m4s