[2024-01-24 13:03:20,409] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:03:20,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:03:20,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference
[2024-01-24 13:03:21,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:03:21,658] [INFO] Task started: Prodigal
[2024-01-24 13:03:21,658] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf10ac97-164c-4c70-ad78-a6bb57b3ab60/GCF_016894345.1_ASM1689434v1_genomic.fna.gz | prodigal -d GCF_016894345.1_ASM1689434v1_genomic.fna/cds.fna -a GCF_016894345.1_ASM1689434v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:03:32,171] [INFO] Task succeeded: Prodigal
[2024-01-24 13:03:32,172] [INFO] Task started: HMMsearch
[2024-01-24 13:03:32,172] [INFO] Running command: hmmsearch --tblout GCF_016894345.1_ASM1689434v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/reference_markers.hmm GCF_016894345.1_ASM1689434v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:03:32,425] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:03:32,427] [INFO] Found 6/6 markers.
[2024-01-24 13:03:32,457] [INFO] Query marker FASTA was written to GCF_016894345.1_ASM1689434v1_genomic.fna/markers.fasta
[2024-01-24 13:03:32,458] [INFO] Task started: Blastn
[2024-01-24 13:03:32,458] [INFO] Running command: blastn -query GCF_016894345.1_ASM1689434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/reference_markers.fasta -out GCF_016894345.1_ASM1689434v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:33,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:33,206] [INFO] Selected 17 target genomes.
[2024-01-24 13:03:33,206] [INFO] Target genome list was writen to GCF_016894345.1_ASM1689434v1_genomic.fna/target_genomes.txt
[2024-01-24 13:03:33,213] [INFO] Task started: fastANI
[2024-01-24 13:03:33,214] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf10ac97-164c-4c70-ad78-a6bb57b3ab60/GCF_016894345.1_ASM1689434v1_genomic.fna.gz --refList GCF_016894345.1_ASM1689434v1_genomic.fna/target_genomes.txt --output GCF_016894345.1_ASM1689434v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:03:42,002] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:42,003] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:03:42,003] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:03:42,028] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:03:42,028] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:03:42,028] [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
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	80.5223	476	968	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	80.4431	445	968	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	79.4296	418	968	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	79.2566	332	968	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	79.2353	334	968	95	below_threshold
Neisseria shayeganii	strain=871	GCA_000226875.1	607712	607712	type	True	79.166	338	968	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	78.9536	326	968	95	below_threshold
Neisseria animalis	strain=ATCC 49930	GCA_008806995.1	492	492	type	True	78.5362	205	968	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	78.5349	232	968	95	below_threshold
Neisseria animalis	strain=NCTC10212	GCA_900636515.1	492	492	type	True	78.4394	207	968	95	below_threshold
Bergeriella denitrificans	strain=NCTC10295	GCA_900453875.1	494	494	type	True	78.4065	277	968	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.4026	266	968	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	78.3388	262	968	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	78.2823	222	968	95	below_threshold
Neisseria zalophi	strain=ATCC BAA-2455	GCA_008807015.1	640030	640030	type	True	78.0407	161	968	95	below_threshold
Stenoxybacter acetivorans	strain=DSM 19021	GCA_000745895.1	422441	422441	type	True	77.082	227	968	95	below_threshold
Chromobacterium piscinae	strain=DSM 23278	GCA_021129175.1	686831	686831	type	True	76.1704	108	968	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:03:42,030] [INFO] DFAST Taxonomy check result was written to GCF_016894345.1_ASM1689434v1_genomic.fna/tc_result.tsv
[2024-01-24 13:03:42,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:03:42,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:03:42,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/checkm_data
[2024-01-24 13:03:42,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:03:42,064] [INFO] Task started: CheckM
[2024-01-24 13:03:42,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016894345.1_ASM1689434v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016894345.1_ASM1689434v1_genomic.fna/checkm_input GCF_016894345.1_ASM1689434v1_genomic.fna/checkm_result
[2024-01-24 13:04:15,996] [INFO] Task succeeded: CheckM
[2024-01-24 13:04:15,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:04:16,023] [INFO] ===== Completeness check finished =====
[2024-01-24 13:04:16,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:04:16,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016894345.1_ASM1689434v1_genomic.fna/markers.fasta)
[2024-01-24 13:04:16,024] [INFO] Task started: Blastn
[2024-01-24 13:04:16,024] [INFO] Running command: blastn -query GCF_016894345.1_ASM1689434v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02232501-6b57-4108-a3a4-2416f800eee6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016894345.1_ASM1689434v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:04:17,327] [INFO] Task succeeded: Blastn
[2024-01-24 13:04:17,332] [INFO] Selected 16 target genomes.
[2024-01-24 13:04:17,332] [INFO] Target genome list was writen to GCF_016894345.1_ASM1689434v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:04:17,346] [INFO] Task started: fastANI
[2024-01-24 13:04:17,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf10ac97-164c-4c70-ad78-a6bb57b3ab60/GCF_016894345.1_ASM1689434v1_genomic.fna.gz --refList GCF_016894345.1_ASM1689434v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016894345.1_ASM1689434v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:28,507] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:28,521] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:28,521] [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
GCA_016894345.1	s__26B sp016894345	100.0	967	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__26B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004341385.1	s__Neisseria suis	80.4279	446	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.29	97.17	0.93	0.92	3	-
GCF_014055005.1	s__Neisseria dentiae	79.2376	335	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_000226875.1	s__Eikenella shayeganii	79.1544	338	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	96.47	96.47	0.85	0.85	2	-
GCF_900187305.1	s__Neisseria zoodegmatis	78.6076	269	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900636515.1	s__Neisseria animalis	78.5558	203	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_002237445.1	s__Neisseria sp002237445	78.3976	244	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_002108505.1	s__Neisseria dumasiana	78.3551	261	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_001592185.1	s__Neisseria denitrificans	78.3097	221	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005886145.1	s__Neisseria sp000090875	78.1906	208	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_900637855.1	s__Neisseria animaloris	78.1368	236	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	-
GCF_008807015.1	s__Neisseria zalophi	77.9641	160	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590725.1	s__Snodgrassella sp001590725	77.1976	161	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Snodgrassella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745895.1	s__Stenoxybacter acetivorans	77.1043	225	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Stenoxybacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007705.1	s__Chromobacterium violaceum	77.0668	114	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	98.58	98.16	0.94	0.91	26	-
GCF_011601295.1	s__Chromobacterium vaccinii_A	76.2074	109	968	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Chromobacterium	95.0	95.84	95.77	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:28,524] [INFO] GTDB search result was written to GCF_016894345.1_ASM1689434v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:28,525] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:28,532] [INFO] DFAST_QC result json was written to GCF_016894345.1_ASM1689434v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:28,532] [INFO] DFAST_QC completed!
[2024-01-24 13:04:28,532] [INFO] Total running time: 0h1m8s