[2024-01-24 12:14:10,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:10,069] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:10,069] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference
[2024-01-24 12:14:11,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:11,396] [INFO] Task started: Prodigal
[2024-01-24 12:14:11,396] [INFO] Running command: gunzip -c /var/lib/cwl/stg926ee3e9-adc3-4c8f-8fff-e89b29a97ead/GCF_008807015.1_ASM880701v1_genomic.fna.gz | prodigal -d GCF_008807015.1_ASM880701v1_genomic.fna/cds.fna -a GCF_008807015.1_ASM880701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:17,688] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:17,688] [INFO] Task started: HMMsearch
[2024-01-24 12:14:17,688] [INFO] Running command: hmmsearch --tblout GCF_008807015.1_ASM880701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/reference_markers.hmm GCF_008807015.1_ASM880701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:17,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:17,964] [INFO] Found 6/6 markers.
[2024-01-24 12:14:17,989] [INFO] Query marker FASTA was written to GCF_008807015.1_ASM880701v1_genomic.fna/markers.fasta
[2024-01-24 12:14:17,989] [INFO] Task started: Blastn
[2024-01-24 12:14:17,989] [INFO] Running command: blastn -query GCF_008807015.1_ASM880701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/reference_markers.fasta -out GCF_008807015.1_ASM880701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:18,689] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:18,694] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:18,694] [INFO] Target genome list was writen to GCF_008807015.1_ASM880701v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:18,704] [INFO] Task started: fastANI
[2024-01-24 12:14:18,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg926ee3e9-adc3-4c8f-8fff-e89b29a97ead/GCF_008807015.1_ASM880701v1_genomic.fna.gz --refList GCF_008807015.1_ASM880701v1_genomic.fna/target_genomes.txt --output GCF_008807015.1_ASM880701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:27,935] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:27,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:27,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:27,950] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:27,951] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:27,951] [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 zalophi	strain=ATCC BAA-2455	GCA_008807015.1	640030	640030	type	True	100.0	805	807	95	conclusive
Neisseria zoodegmatis	strain=NCTC12230	GCA_900187305.1	326523	326523	type	True	79.4752	383	807	95	below_threshold
Neisseria animaloris	strain=NCTC12228	GCA_900637855.1	326522	326522	type	True	79.4161	344	807	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	79.4142	390	807	95	below_threshold
Neisseria zoodegmatis	strain=DSM 21643	GCA_002108575.1	326523	326523	type	True	79.3782	379	807	95	below_threshold
Neisseria dumasiana	strain=93087	GCA_002108505.1	1931275	1931275	type	True	79.3155	379	807	95	below_threshold
Neisseria weaveri	strain=NCTC12742	GCA_900638685.1	28091	28091	type	True	79.2148	268	807	95	below_threshold
Neisseria animaloris	strain=DSM 21642	GCA_002108605.1	326522	326522	type	True	79.0243	329	807	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_014055005.1	194197	194197	type	True	78.8511	340	807	95	below_threshold
Neisseria weaveri	strain=LMG 5135	GCA_000224255.2	28091	28091	type	True	78.762	252	807	95	below_threshold
Neisseria dentiae	strain=NCTC13012	GCA_900453685.1	194197	194197	type	True	78.7477	344	807	95	below_threshold
Neisseria dentiae	strain=DSM 19151	GCA_002108595.1	194197	194197	type	True	78.6396	333	807	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.324	317	807	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.267	280	807	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	78.0947	175	807	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	78.0286	258	807	95	below_threshold
Bergeriella denitrificans	strain=NBRC 102155	GCA_001592185.1	494	494	type	True	77.9337	191	807	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,953] [INFO] DFAST Taxonomy check result was written to GCF_008807015.1_ASM880701v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:27,953] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:27,954] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:27,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/checkm_data
[2024-01-24 12:14:27,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:27,985] [INFO] Task started: CheckM
[2024-01-24 12:14:27,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008807015.1_ASM880701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008807015.1_ASM880701v1_genomic.fna/checkm_input GCF_008807015.1_ASM880701v1_genomic.fna/checkm_result
[2024-01-24 12:14:53,902] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:53,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,924] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:53,924] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:53,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008807015.1_ASM880701v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:53,925] [INFO] Task started: Blastn
[2024-01-24 12:14:53,925] [INFO] Running command: blastn -query GCF_008807015.1_ASM880701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fb9ab54-3042-42ae-8f63-dc3dfc5509aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_008807015.1_ASM880701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:55,185] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:55,189] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:55,190] [INFO] Target genome list was writen to GCF_008807015.1_ASM880701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:55,204] [INFO] Task started: fastANI
[2024-01-24 12:14:55,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg926ee3e9-adc3-4c8f-8fff-e89b29a97ead/GCF_008807015.1_ASM880701v1_genomic.fna.gz --refList GCF_008807015.1_ASM880701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008807015.1_ASM880701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:02,726] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:02,743] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:02,743] [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_008807015.1	s__Neisseria zalophi	100.0	806	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900187305.1	s__Neisseria zoodegmatis	79.5544	383	807	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	79.3632	339	807	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	79.2988	379	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_900638685.1	s__Neisseria weaveri	79.2433	264	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.19	98.86	0.98	0.97	8	-
GCF_014055005.1	s__Neisseria dentiae	78.809	340	807	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	78.3327	304	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.59	98.59	0.96	0.96	3	-
GCF_001308015.1	s__Neisseria sp001308015	78.324	239	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451175.1	s__Neisseria potus	78.1792	175	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592185.1	s__Neisseria denitrificans	77.9573	189	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001618085.1	s__Neisseria flavescens_C	77.9406	202	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.4709	96.21	96.21	0.92	0.92	2	-
GCF_003045025.1	s__Neisseria subflava_A	77.9032	213	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.3115	96.25	95.58	0.94	0.91	14	-
GCF_000260655.1	s__Neisseria sicca_B	77.7661	179	807	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
GCF_001027865.1	s__Neisseria arctica	77.7598	208	807	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 12:15:02,745] [INFO] GTDB search result was written to GCF_008807015.1_ASM880701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:02,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:02,749] [INFO] DFAST_QC result json was written to GCF_008807015.1_ASM880701v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:02,750] [INFO] DFAST_QC completed!
[2024-01-24 12:15:02,750] [INFO] Total running time: 0h0m53s