[2024-01-24 14:55:35,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:35,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:35,685] [INFO] DQC Reference Directory: /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference
[2024-01-24 14:55:37,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:37,069] [INFO] Task started: Prodigal
[2024-01-24 14:55:37,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg92997d77-001e-4f31-8c95-4c720efb2159/GCF_014054985.1_ASM1405498v1_genomic.fna.gz | prodigal -d GCF_014054985.1_ASM1405498v1_genomic.fna/cds.fna -a GCF_014054985.1_ASM1405498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:45,464] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:45,464] [INFO] Task started: HMMsearch
[2024-01-24 14:55:45,464] [INFO] Running command: hmmsearch --tblout GCF_014054985.1_ASM1405498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/reference_markers.hmm GCF_014054985.1_ASM1405498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:45,838] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:45,839] [INFO] Found 6/6 markers.
[2024-01-24 14:55:45,937] [INFO] Query marker FASTA was written to GCF_014054985.1_ASM1405498v1_genomic.fna/markers.fasta
[2024-01-24 14:55:45,938] [INFO] Task started: Blastn
[2024-01-24 14:55:45,938] [INFO] Running command: blastn -query GCF_014054985.1_ASM1405498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/reference_markers.fasta -out GCF_014054985.1_ASM1405498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:46,580] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:46,584] [INFO] Selected 16 target genomes.
[2024-01-24 14:55:46,585] [INFO] Target genome list was writen to GCF_014054985.1_ASM1405498v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:46,592] [INFO] Task started: fastANI
[2024-01-24 14:55:46,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg92997d77-001e-4f31-8c95-4c720efb2159/GCF_014054985.1_ASM1405498v1_genomic.fna.gz --refList GCF_014054985.1_ASM1405498v1_genomic.fna/target_genomes.txt --output GCF_014054985.1_ASM1405498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:00,584] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:00,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:00,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:00,598] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:56:00,598] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:56:00,598] [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=DSM 18271	GCA_014054985.1	505	505	type	True	100.0	804	806	95	inconclusive
Kingella oralis	strain=ATCC 51147	GCA_000160435.1	505	505	type	True	99.9867	797	806	95	inconclusive
Kingella bonacorsii	strain=Marseille-Q4569	GCA_016623605.1	2796361	2796361	type	True	96.4198	730	806	95	inconclusive
Neisseria bacilliformis	strain=DSM 23338	GCA_014055025.1	267212	267212	type	True	79.9075	294	806	95	below_threshold
Neisseria bacilliformis	strain=ATCC BAA-1200	GCA_000194925.1	267212	267212	type	True	79.7543	282	806	95	below_threshold
Kingella denitrificans	strain=FDAARGOS_1060	GCA_016127355.1	502	502	type	True	79.5084	317	806	95	below_threshold
Kingella denitrificans	strain=ATCC 33394	GCA_000190695.1	502	502	type	True	79.2292	310	806	95	below_threshold
Kingella potus	strain=NCTC13336	GCA_900451175.1	265175	265175	type	True	78.9325	254	806	95	below_threshold
Kingella potus	strain=3/SID/1128	GCA_022870985.1	265175	265175	type	True	78.8605	255	806	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	78.4733	247	806	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	78.1133	234	806	95	below_threshold
Neisseria dumasiana	strain=LMG 30012	GCA_022870885.1	1931275	1931275	type	True	78.06	206	806	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	78.0447	287	806	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	77.9402	288	806	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	77.8203	263	806	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	77.7313	228	806	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:00,600] [INFO] DFAST Taxonomy check result was written to GCF_014054985.1_ASM1405498v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:00,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:00,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:00,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/checkm_data
[2024-01-24 14:56:00,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:00,634] [INFO] Task started: CheckM
[2024-01-24 14:56:00,635] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014054985.1_ASM1405498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014054985.1_ASM1405498v1_genomic.fna/checkm_input GCF_014054985.1_ASM1405498v1_genomic.fna/checkm_result
[2024-01-24 14:56:30,656] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:30,657] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:30,678] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:30,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:30,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014054985.1_ASM1405498v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:30,680] [INFO] Task started: Blastn
[2024-01-24 14:56:30,680] [INFO] Running command: blastn -query GCF_014054985.1_ASM1405498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge1a7723e-0746-44ed-94ff-0150cc601b7a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014054985.1_ASM1405498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:31,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:31,671] [INFO] Selected 12 target genomes.
[2024-01-24 14:56:31,671] [INFO] Target genome list was writen to GCF_014054985.1_ASM1405498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:31,682] [INFO] Task started: fastANI
[2024-01-24 14:56:31,682] [INFO] Running command: fastANI --query /var/lib/cwl/stg92997d77-001e-4f31-8c95-4c720efb2159/GCF_014054985.1_ASM1405498v1_genomic.fna.gz --refList GCF_014054985.1_ASM1405498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014054985.1_ASM1405498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:41,759] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:41,774] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:41,774] [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	100.0	805	806	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	91.1916	347	806	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	79.9847	293	806	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	79.2511	309	806	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	78.9463	255	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990355.1	s__Eikenella corrodens_B	78.8718	249	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001648475.1	s__Eikenella halliae	78.8673	247	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Eikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237445.1	s__Neisseria sp002237445	78.6802	268	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	99.69	99.69	0.98	0.98	2	-
GCF_014054525.1	s__Alysiella filiformis	78.3343	282	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008807015.1	s__Neisseria zalophi	78.2093	90	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745955.1	s__Alysiella crassa	77.6942	271	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_002108505.1	s__Neisseria dumasiana	77.6862	202	806	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	97.54	97.26	0.91	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:41,776] [INFO] GTDB search result was written to GCF_014054985.1_ASM1405498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:41,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:41,781] [INFO] DFAST_QC result json was written to GCF_014054985.1_ASM1405498v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:41,782] [INFO] DFAST_QC completed!
[2024-01-24 14:56:41,782] [INFO] Total running time: 0h1m6s