[2024-01-25 19:05:05,464] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:05,468] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:05,469] [INFO] DQC Reference Directory: /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference
[2024-01-25 19:05:06,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:06,659] [INFO] Task started: Prodigal
[2024-01-25 19:05:06,659] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6bd8295-3dff-4ef9-bdf3-2e28b1b1f08c/GCF_002951835.1_ASM295183v1_genomic.fna.gz | prodigal -d GCF_002951835.1_ASM295183v1_genomic.fna/cds.fna -a GCF_002951835.1_ASM295183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:13,364] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:13,364] [INFO] Task started: HMMsearch
[2024-01-25 19:05:13,365] [INFO] Running command: hmmsearch --tblout GCF_002951835.1_ASM295183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/reference_markers.hmm GCF_002951835.1_ASM295183v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:13,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:13,566] [INFO] Found 6/6 markers.
[2024-01-25 19:05:13,590] [INFO] Query marker FASTA was written to GCF_002951835.1_ASM295183v1_genomic.fna/markers.fasta
[2024-01-25 19:05:13,590] [INFO] Task started: Blastn
[2024-01-25 19:05:13,590] [INFO] Running command: blastn -query GCF_002951835.1_ASM295183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/reference_markers.fasta -out GCF_002951835.1_ASM295183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:14,208] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:14,210] [INFO] Selected 14 target genomes.
[2024-01-25 19:05:14,211] [INFO] Target genome list was writen to GCF_002951835.1_ASM295183v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:14,238] [INFO] Task started: fastANI
[2024-01-25 19:05:14,239] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bd8295-3dff-4ef9-bdf3-2e28b1b1f08c/GCF_002951835.1_ASM295183v1_genomic.fna.gz --refList GCF_002951835.1_ASM295183v1_genomic.fna/target_genomes.txt --output GCF_002951835.1_ASM295183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:24,034] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:24,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:24,034] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:24,044] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 19:05:24,044] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:24,044] [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
Simonsiella muelleri	strain=ATCC 29453	GCA_002951835.1	72	72	type	True	100.0	813	823	95	conclusive
Simonsiella muelleri	strain=DSM 2579	GCA_020162275.1	72	72	type	True	99.9897	807	823	95	conclusive
Simonsiella muelleri	strain=ATCC 29453	GCA_000163775.2	72	72	type	True	99.8943	764	823	95	conclusive
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	80.384	269	823	95	below_threshold
Kingella kingae	strain=NCTC10529	GCA_900475905.1	504	504	type	True	80.3808	270	823	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	79.9554	433	823	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	79.9131	453	823	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	79.8734	430	823	95	below_threshold
Kingella kingae	strain=ATCC 23330	GCA_000213535.1	504	504	type	True	79.8309	268	823	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_020162295.1	194196	194196	type	True	79.3403	316	823	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_014054525.1	194196	194196	type	True	79.299	327	823	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	78.3294	72	823	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	78.0585	74	823	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	78.0412	83	823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:24,045] [INFO] DFAST Taxonomy check result was written to GCF_002951835.1_ASM295183v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:24,046] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:24,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:24,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/checkm_data
[2024-01-25 19:05:24,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:24,073] [INFO] Task started: CheckM
[2024-01-25 19:05:24,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002951835.1_ASM295183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002951835.1_ASM295183v1_genomic.fna/checkm_input GCF_002951835.1_ASM295183v1_genomic.fna/checkm_result
[2024-01-25 19:05:49,591] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:49,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:49,609] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:49,609] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:49,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002951835.1_ASM295183v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:49,610] [INFO] Task started: Blastn
[2024-01-25 19:05:49,610] [INFO] Running command: blastn -query GCF_002951835.1_ASM295183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40cc038c-73f3-41f5-9203-54cadc03e31e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002951835.1_ASM295183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:50,613] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:50,616] [INFO] Selected 8 target genomes.
[2024-01-25 19:05:50,616] [INFO] Target genome list was writen to GCF_002951835.1_ASM295183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:50,627] [INFO] Task started: fastANI
[2024-01-25 19:05:50,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6bd8295-3dff-4ef9-bdf3-2e28b1b1f08c/GCF_002951835.1_ASM295183v1_genomic.fna.gz --refList GCF_002951835.1_ASM295183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002951835.1_ASM295183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:56,003] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:56,009] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:56,009] [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_002951835.1	s__Simonsiella muelleri	100.0	813	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Simonsiella	95.0	99.93	99.93	0.98	0.98	2	conclusive
GCF_000745955.1	s__Alysiella crassa	79.8857	432	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_900111845.1	s__Kingella kingae	79.8668	257	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCF_000751855.1	s__Kingella negevensis	79.6287	249	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_014054525.1	s__Alysiella filiformis	79.2005	328	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014054985.1	s__Kingella_B oralis	77.8699	175	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	98.22	96.45	0.95	0.91	3	-
GCF_000193795.1	s__Neisseria lactamica_A	77.3093	73	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260655.1	s__Neisseria sicca_B	77.2116	62	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:56,010] [INFO] GTDB search result was written to GCF_002951835.1_ASM295183v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:56,011] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:56,013] [INFO] DFAST_QC result json was written to GCF_002951835.1_ASM295183v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:56,013] [INFO] DFAST_QC completed!
[2024-01-25 19:05:56,013] [INFO] Total running time: 0h0m51s