[2024-01-24 14:22:04,007] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,010] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference
[2024-01-24 14:22:05,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,326] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg7814897f-8c8a-48fe-9fca-a1f77cf7f22f/GCF_900637855.1_52683_F03_genomic.fna.gz | prodigal -d GCF_900637855.1_52683_F03_genomic.fna/cds.fna -a GCF_900637855.1_52683_F03_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:12,827] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:12,828] [INFO] Task started: HMMsearch
[2024-01-24 14:22:12,828] [INFO] Running command: hmmsearch --tblout GCF_900637855.1_52683_F03_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/reference_markers.hmm GCF_900637855.1_52683_F03_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:13,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:13,097] [INFO] Found 6/6 markers.
[2024-01-24 14:22:13,126] [INFO] Query marker FASTA was written to GCF_900637855.1_52683_F03_genomic.fna/markers.fasta
[2024-01-24 14:22:13,126] [INFO] Task started: Blastn
[2024-01-24 14:22:13,127] [INFO] Running command: blastn -query GCF_900637855.1_52683_F03_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/reference_markers.fasta -out GCF_900637855.1_52683_F03_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:13,867] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:13,870] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:13,871] [INFO] Target genome list was writen to GCF_900637855.1_52683_F03_genomic.fna/target_genomes.txt
[2024-01-24 14:22:13,877] [INFO] Task started: fastANI
[2024-01-24 14:22:13,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg7814897f-8c8a-48fe-9fca-a1f77cf7f22f/GCF_900637855.1_52683_F03_genomic.fna.gz --refList GCF_900637855.1_52683_F03_genomic.fna/target_genomes.txt --output GCF_900637855.1_52683_F03_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:21,958] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:21,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:21,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:21,971] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:21,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:21,972] [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 animaloris	strain=NCTC12228	GCA_900637855.1	326522	326522	type	True	100.0	777	779	95	conclusive
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	99.9707	759	779	95	conclusive
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	87.2882	476	779	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	87.0815	462	779	95	below_threshold
Neisseria zoodegmatis	strain=NCTC12230	GCA_900187305.1	326523	326523	type	True	86.5632	473	779	95	below_threshold
Neisseria zoodegmatis	strain=DSM 21643	GCA_002108575.1	326523	326523	type	True	86.4618	465	779	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	84.1084	349	779	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	79.8803	414	779	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	79.4414	362	779	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	79.2478	295	779	95	below_threshold
Neisseria cinerea	strain=NCTC10294	GCA_900475315.1	483	483	type	True	79.2399	250	779	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	79.1847	291	779	95	below_threshold
Neisseria flavescens	strain=ATCC 13120	GCA_005221285.1	484	484	type	True	78.6929	311	779	95	below_threshold
Neisseria flavescens	strain=NCTC8263	GCA_900453805.1	484	484	type	True	78.6866	313	779	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:21,973] [INFO] DFAST Taxonomy check result was written to GCF_900637855.1_52683_F03_genomic.fna/tc_result.tsv
[2024-01-24 14:22:21,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:21,974] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:21,974] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/checkm_data
[2024-01-24 14:22:21,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:22,002] [INFO] Task started: CheckM
[2024-01-24 14:22:22,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637855.1_52683_F03_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637855.1_52683_F03_genomic.fna/checkm_input GCF_900637855.1_52683_F03_genomic.fna/checkm_result
[2024-01-24 14:22:48,648] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:48,649] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:48,669] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:48,670] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:48,670] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637855.1_52683_F03_genomic.fna/markers.fasta)
[2024-01-24 14:22:48,671] [INFO] Task started: Blastn
[2024-01-24 14:22:48,671] [INFO] Running command: blastn -query GCF_900637855.1_52683_F03_genomic.fna/markers.fasta -db /var/lib/cwl/stgff0c3629-8c19-4847-a9e5-bf6311e9e33b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637855.1_52683_F03_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:49,922] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:49,925] [INFO] Selected 16 target genomes.
[2024-01-24 14:22:49,925] [INFO] Target genome list was writen to GCF_900637855.1_52683_F03_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:49,936] [INFO] Task started: fastANI
[2024-01-24 14:22:49,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg7814897f-8c8a-48fe-9fca-a1f77cf7f22f/GCF_900637855.1_52683_F03_genomic.fna.gz --refList GCF_900637855.1_52683_F03_genomic.fna/target_genomes_gtdb.txt --output GCF_900637855.1_52683_F03_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:58,726] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:58,739] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:58,739] [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_900637855.1	s__Neisseria animaloris	100.0	778	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.11	0.97	0.94	5	conclusive
GCF_002108505.1	s__Neisseria dumasiana	87.0571	465	779	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	86.6441	471	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.30	96.60	0.95	0.90	3	-
GCF_900638685.1	s__Neisseria weaveri	84.0091	365	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_900636765.1	s__Neisseria canis	83.3088	341	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014055005.1	s__Neisseria dentiae	81.4258	446	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.99	99.98	1.00	1.00	3	-
GCF_014297595.1	s__Neisseria musculi	80.0379	420	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_900636515.1	s__Neisseria animalis	79.5344	301	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	99.99	0.99	0.99	3	-
GCF_005886145.1	s__Neisseria sp000090875	79.3265	356	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.69	97.41	0.97	0.94	3	-
GCF_008807015.1	s__Neisseria zalophi	79.2953	337	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952795.1	s__Neisseria sp000952795	79.0884	301	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.4916	98.25	96.69	0.90	0.83	3	-
GCF_000193735.1	s__Neisseria sicca_E	78.9852	300	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193795.1	s__Neisseria lactamica_A	78.8009	258	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005221285.1	s__Neisseria flavescens	78.7613	309	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.29	96.65	0.97	0.93	6	-
GCF_001618085.1	s__Neisseria flavescens_C	78.5771	286	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003044645.1	s__Neisseria subflava_B	78.4998	284	779	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.654	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:58,740] [INFO] GTDB search result was written to GCF_900637855.1_52683_F03_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:58,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:58,744] [INFO] DFAST_QC result json was written to GCF_900637855.1_52683_F03_genomic.fna/dqc_result.json
[2024-01-24 14:22:58,744] [INFO] DFAST_QC completed!
[2024-01-24 14:22:58,744] [INFO] Total running time: 0h0m55s