[2024-01-24 13:46:26,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:26,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:26,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference
[2024-01-24 13:46:27,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:27,736] [INFO] Task started: Prodigal
[2024-01-24 13:46:27,737] [INFO] Running command: gunzip -c /var/lib/cwl/stg05c28455-52e6-4f0a-af84-0fc5f39a8088/GCF_000160435.1_ASM16043v1_genomic.fna.gz | prodigal -d GCF_000160435.1_ASM16043v1_genomic.fna/cds.fna -a GCF_000160435.1_ASM16043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:35,130] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:35,130] [INFO] Task started: HMMsearch
[2024-01-24 13:46:35,130] [INFO] Running command: hmmsearch --tblout GCF_000160435.1_ASM16043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/reference_markers.hmm GCF_000160435.1_ASM16043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:35,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:35,416] [INFO] Found 6/6 markers.
[2024-01-24 13:46:35,436] [INFO] Query marker FASTA was written to GCF_000160435.1_ASM16043v1_genomic.fna/markers.fasta
[2024-01-24 13:46:35,437] [INFO] Task started: Blastn
[2024-01-24 13:46:35,437] [INFO] Running command: blastn -query GCF_000160435.1_ASM16043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/reference_markers.fasta -out GCF_000160435.1_ASM16043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:36,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:36,043] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:36,043] [INFO] Target genome list was writen to GCF_000160435.1_ASM16043v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:36,058] [INFO] Task started: fastANI
[2024-01-24 13:46:36,059] [INFO] Running command: fastANI --query /var/lib/cwl/stg05c28455-52e6-4f0a-af84-0fc5f39a8088/GCF_000160435.1_ASM16043v1_genomic.fna.gz --refList GCF_000160435.1_ASM16043v1_genomic.fna/target_genomes.txt --output GCF_000160435.1_ASM16043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:49,647] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:49,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:49,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:49,658] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:46:49,658] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:49,658] [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
Kingella oralis	strain=ATCC 51147	GCA_000160435.1	505	505	type	True	100.0	800	800	95	inconclusive
Kingella oralis	strain=DSM 18271	GCA_014054985.1	505	505	type	True	99.9897	795	800	95	inconclusive
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	96.3558	723	800	95	inconclusive
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	79.6894	305	800	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	79.566	302	800	95	below_threshold
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	79.3562	310	800	95	below_threshold
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	79.3505	312	800	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	78.8501	243	800	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	78.656	252	800	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	78.2133	257	800	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	77.9076	204	800	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	77.8778	265	800	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	77.8774	284	800	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	77.8378	291	800	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	77.756	244	800	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	77.6636	238	800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:49,659] [INFO] DFAST Taxonomy check result was written to GCF_000160435.1_ASM16043v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:49,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:49,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:49,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/checkm_data
[2024-01-24 13:46:49,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:49,688] [INFO] Task started: CheckM
[2024-01-24 13:46:49,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000160435.1_ASM16043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000160435.1_ASM16043v1_genomic.fna/checkm_input GCF_000160435.1_ASM16043v1_genomic.fna/checkm_result
[2024-01-24 13:47:13,809] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:13,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:13,822] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:13,822] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:13,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000160435.1_ASM16043v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:13,822] [INFO] Task started: Blastn
[2024-01-24 13:47:13,822] [INFO] Running command: blastn -query GCF_000160435.1_ASM16043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccf2d95-8b21-4f11-a0dc-4567db6e779c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000160435.1_ASM16043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:14,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:14,718] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:14,718] [INFO] Target genome list was writen to GCF_000160435.1_ASM16043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:14,726] [INFO] Task started: fastANI
[2024-01-24 13:47:14,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg05c28455-52e6-4f0a-af84-0fc5f39a8088/GCF_000160435.1_ASM16043v1_genomic.fna.gz --refList GCF_000160435.1_ASM16043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000160435.1_ASM16043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:23,168] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:23,176] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:23,176] [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_014054985.1	s__Kingella_B oralis	99.9897	795	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	conclusive
GCA_905373195.1	s__Kingella_B oralis_A	91.2454	346	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014055025.1	s__Neisseria bacilliformis	79.7017	304	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	98.33	96.96	0.94	0.89	4	-
GCF_000190695.1	s__Kingella_A denitrificans	79.3563	310	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_A	95.0	98.63	96.04	0.97	0.93	4	-
GCF_900451175.1	s__Neisseria potus	78.7813	249	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237445.1	s__Neisseria sp002237445	78.7018	285	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_001648475.1	s__Eikenella halliae	78.63	257	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	78.5979	254	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014054525.1	s__Alysiella filiformis	78.2941	281	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002108505.1	s__Neisseria dumasiana	77.8924	209	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
GCF_000745955.1	s__Alysiella crassa	77.8203	274	800	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_008807015.1	s__Neisseria zalophi	77.5138	90	800	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 13:47:23,177] [INFO] GTDB search result was written to GCF_000160435.1_ASM16043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:23,177] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:23,180] [INFO] DFAST_QC result json was written to GCF_000160435.1_ASM16043v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:23,180] [INFO] DFAST_QC completed!
[2024-01-24 13:47:23,180] [INFO] Total running time: 0h0m57s