[2024-01-24 13:28:25,717] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,718] [INFO] DQC Reference Directory: /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference
[2024-01-24 13:28:27,045] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,046] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fb68a93-e5d4-4bed-a7c3-4a1d4c6362c5/GCF_000227765.1_ASM22776v1_genomic.fna.gz | prodigal -d GCF_000227765.1_ASM22776v1_genomic.fna/cds.fna -a GCF_000227765.1_ASM22776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:34,785] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:34,786] [INFO] Task started: HMMsearch
[2024-01-24 13:28:34,786] [INFO] Running command: hmmsearch --tblout GCF_000227765.1_ASM22776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/reference_markers.hmm GCF_000227765.1_ASM22776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:35,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:35,111] [INFO] Found 6/6 markers.
[2024-01-24 13:28:35,145] [INFO] Query marker FASTA was written to GCF_000227765.1_ASM22776v1_genomic.fna/markers.fasta
[2024-01-24 13:28:35,146] [INFO] Task started: Blastn
[2024-01-24 13:28:35,146] [INFO] Running command: blastn -query GCF_000227765.1_ASM22776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/reference_markers.fasta -out GCF_000227765.1_ASM22776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:35,915] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:35,919] [INFO] Selected 16 target genomes.
[2024-01-24 13:28:35,919] [INFO] Target genome list was writen to GCF_000227765.1_ASM22776v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:35,930] [INFO] Task started: fastANI
[2024-01-24 13:28:35,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb68a93-e5d4-4bed-a7c3-4a1d4c6362c5/GCF_000227765.1_ASM22776v1_genomic.fna.gz --refList GCF_000227765.1_ASM22776v1_genomic.fna/target_genomes.txt --output GCF_000227765.1_ASM22776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:47,489] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:47,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:47,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:47,507] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:47,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:47,508] [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 wadsworthii	strain=9715	GCA_000227765.1	607711	607711	type	True	99.996	810	817	95	conclusive
Neisseria canis	strain=ATCC 14687	GCA_002108495.1	493	493	type	True	90.1625	652	817	95	below_threshold
Neisseria canis	strain=NCTC10296	GCA_900636765.1	493	493	type	True	89.985	682	817	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	82.2885	364	817	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	82.0533	357	817	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	78.9518	321	817	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.9216	335	817	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.6467	332	817	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	78.5313	213	817	95	below_threshold
Morococcus cerebrosus	strain=CIP 81.93	GCA_022749515.1	1056807	1056807	type	True	78.5254	242	817	95	below_threshold
Neisseria meningitidis	strain=PartJ-Nmeningitidis-RM8376	GCA_022869645.1	487	487	type	True	78.4714	205	817	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	78.4551	221	817	95	below_threshold
Neisseria elongata	strain=NCTC10660	GCA_900453895.1	495	495	type	True	78.3469	260	817	95	below_threshold
Neisseria elongata subsp. elongata	strain=ATCC 25295	GCA_900113545.1	214482	495	type	True	78.3206	256	817	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	78.0194	220	817	95	below_threshold
Neisseria arctica	strain=KH1503	GCA_022870905.1	1470200	1470200	type	True	77.8257	182	817	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:47,509] [INFO] DFAST Taxonomy check result was written to GCF_000227765.1_ASM22776v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:47,510] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:47,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:47,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/checkm_data
[2024-01-24 13:28:47,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:47,539] [INFO] Task started: CheckM
[2024-01-24 13:28:47,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000227765.1_ASM22776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000227765.1_ASM22776v1_genomic.fna/checkm_input GCF_000227765.1_ASM22776v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,742] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,743] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000227765.1_ASM22776v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,744] [INFO] Task started: Blastn
[2024-01-24 13:29:15,744] [INFO] Running command: blastn -query GCF_000227765.1_ASM22776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1c3c22c-b649-4a86-a30d-d3779c11a378/dqc_reference/reference_markers_gtdb.fasta -out GCF_000227765.1_ASM22776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,847] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,850] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:16,850] [INFO] Target genome list was writen to GCF_000227765.1_ASM22776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,872] [INFO] Task started: fastANI
[2024-01-24 13:29:16,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fb68a93-e5d4-4bed-a7c3-4a1d4c6362c5/GCF_000227765.1_ASM22776v1_genomic.fna.gz --refList GCF_000227765.1_ASM22776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000227765.1_ASM22776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:26,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:26,865] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:26,865] [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_000227765.1	s__Neisseria wadsworthii	99.996	810	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.36	97.06	0.97	0.96	3	conclusive
GCF_001308015.1	s__Neisseria sp001308015	92.6843	733	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636765.1	s__Neisseria canis	90.0077	680	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900187305.1	s__Neisseria zoodegmatis	83.1625	351	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900637855.1	s__Neisseria animaloris	82.2676	316	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_002108505.1	s__Neisseria dumasiana	82.0306	359	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_000193735.1	s__Neisseria sicca_E	79.1771	221	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900636515.1	s__Neisseria animalis	79.1244	228	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_004341385.1	s__Neisseria suis	78.9366	322	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_000260655.1	s__Neisseria sicca_B	78.656	236	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_014297595.1	s__Neisseria musculi	78.639	297	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_005221285.1	s__Neisseria flavescens	78.5407	215	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_008807015.1	s__Neisseria zalophi	78.3956	235	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113545.1	s__Neisseria elongata	78.3379	254	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	96.68	96.06	0.91	0.86	20	-
GCF_013267835.1	s__Neisseria sp000186165	78.1562	242	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0019	96.64	96.07	0.93	0.88	22	-
GCF_003351665.1	s__Neisseria perflava	77.9806	230	817	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.6726	97.77	96.48	0.96	0.95	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:26,867] [INFO] GTDB search result was written to GCF_000227765.1_ASM22776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:26,867] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:26,872] [INFO] DFAST_QC result json was written to GCF_000227765.1_ASM22776v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:26,872] [INFO] DFAST_QC completed!
[2024-01-24 13:29:26,873] [INFO] Total running time: 0h1m1s