[2024-01-24 14:19:45,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,316] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,316] [INFO] DQC Reference Directory: /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference
[2024-01-24 14:19:47,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,130] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg559bb856-fb8e-4ba8-93e6-4db63cd03383/GCF_002108595.1_ASM210859v1_genomic.fna.gz | prodigal -d GCF_002108595.1_ASM210859v1_genomic.fna/cds.fna -a GCF_002108595.1_ASM210859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:54,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:54,439] [INFO] Task started: HMMsearch
[2024-01-24 14:19:54,440] [INFO] Running command: hmmsearch --tblout GCF_002108595.1_ASM210859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/reference_markers.hmm GCF_002108595.1_ASM210859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:54,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:54,716] [INFO] Found 6/6 markers.
[2024-01-24 14:19:54,738] [INFO] Query marker FASTA was written to GCF_002108595.1_ASM210859v1_genomic.fna/markers.fasta
[2024-01-24 14:19:54,738] [INFO] Task started: Blastn
[2024-01-24 14:19:54,738] [INFO] Running command: blastn -query GCF_002108595.1_ASM210859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/reference_markers.fasta -out GCF_002108595.1_ASM210859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:55,522] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:55,524] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:55,525] [INFO] Target genome list was writen to GCF_002108595.1_ASM210859v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:55,564] [INFO] Task started: fastANI
[2024-01-24 14:19:55,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg559bb856-fb8e-4ba8-93e6-4db63cd03383/GCF_002108595.1_ASM210859v1_genomic.fna.gz --refList GCF_002108595.1_ASM210859v1_genomic.fna/target_genomes.txt --output GCF_002108595.1_ASM210859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:15,553] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:15,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:15,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:15,563] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:20:15,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:15,563] [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 dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	100.0	850	859	95	conclusive
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	99.9807	857	859	95	conclusive
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	99.98	859	859	95	conclusive
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	81.9706	498	859	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	81.892	510	859	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	80.8222	497	859	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	80.7181	526	859	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	80.5234	517	859	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.8981	397	859	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.8893	391	859	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	79.8289	333	859	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	79.7818	342	859	95	below_threshold
Neisseria zalophi	strain=ATCC BAA-2455	GCA_008807015.1	640030	640030	type	True	78.6385	333	859	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:15,564] [INFO] DFAST Taxonomy check result was written to GCF_002108595.1_ASM210859v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:15,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:15,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:15,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/checkm_data
[2024-01-24 14:20:15,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:15,593] [INFO] Task started: CheckM
[2024-01-24 14:20:15,593] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002108595.1_ASM210859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002108595.1_ASM210859v1_genomic.fna/checkm_input GCF_002108595.1_ASM210859v1_genomic.fna/checkm_result
[2024-01-24 14:20:39,818] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:39,819] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:39,832] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:39,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:39,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002108595.1_ASM210859v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:39,832] [INFO] Task started: Blastn
[2024-01-24 14:20:39,832] [INFO] Running command: blastn -query GCF_002108595.1_ASM210859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg890ac1e4-3744-43d7-be93-18c82b89dbc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002108595.1_ASM210859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:41,262] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:41,265] [INFO] Selected 14 target genomes.
[2024-01-24 14:20:41,265] [INFO] Target genome list was writen to GCF_002108595.1_ASM210859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:41,273] [INFO] Task started: fastANI
[2024-01-24 14:20:41,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg559bb856-fb8e-4ba8-93e6-4db63cd03383/GCF_002108595.1_ASM210859v1_genomic.fna.gz --refList GCF_002108595.1_ASM210859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002108595.1_ASM210859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:55,139] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:55,147] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:55,148] [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_014055005.1	s__Neisseria dentiae	99.9807	857	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	conclusive
GCF_014297595.1	s__Neisseria musculi	86.756	646	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_002108505.1	s__Neisseria dumasiana	81.9956	495	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900187305.1	s__Neisseria zoodegmatis	81.995	518	859	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	81.1004	431	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_004341385.1	s__Neisseria suis	80.7833	501	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_001592185.1	s__Neisseria denitrificans	80.6211	357	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002216145.1	s__Neisseria chenwenguii	80.2585	455	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.73	99.73	0.96	0.96	2	-
GCF_900638685.1	s__Neisseria weaveri	80.0822	316	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_014055025.1	s__Neisseria bacilliformis	80.0509	415	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_005886145.1	s__Neisseria sp000090875	79.922	425	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_900636515.1	s__Neisseria animalis	79.8126	334	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_014054945.1	s__Neisseria sicca	79.2934	394	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	99.97	99.97	1.00	1.00	2	-
GCF_008807015.1	s__Neisseria zalophi	78.6542	332	859	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:55,149] [INFO] GTDB search result was written to GCF_002108595.1_ASM210859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:55,149] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:55,152] [INFO] DFAST_QC result json was written to GCF_002108595.1_ASM210859v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:55,152] [INFO] DFAST_QC completed!
[2024-01-24 14:20:55,152] [INFO] Total running time: 0h1m10s