[2024-01-24 15:10:40,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:40,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:40,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference
[2024-01-24 15:10:42,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,375] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,376] [INFO] Running command: gunzip -c /var/lib/cwl/stgff7e82ab-0a54-4dc4-b0f7-c0ebe8c6e37b/GCF_020162275.1_ASM2016227v1_genomic.fna.gz | prodigal -d GCF_020162275.1_ASM2016227v1_genomic.fna/cds.fna -a GCF_020162275.1_ASM2016227v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:50,377] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:50,378] [INFO] Task started: HMMsearch
[2024-01-24 15:10:50,378] [INFO] Running command: hmmsearch --tblout GCF_020162275.1_ASM2016227v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/reference_markers.hmm GCF_020162275.1_ASM2016227v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:50,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:50,664] [INFO] Found 6/6 markers.
[2024-01-24 15:10:50,697] [INFO] Query marker FASTA was written to GCF_020162275.1_ASM2016227v1_genomic.fna/markers.fasta
[2024-01-24 15:10:50,698] [INFO] Task started: Blastn
[2024-01-24 15:10:50,698] [INFO] Running command: blastn -query GCF_020162275.1_ASM2016227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/reference_markers.fasta -out GCF_020162275.1_ASM2016227v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:51,404] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:51,407] [INFO] Selected 14 target genomes.
[2024-01-24 15:10:51,407] [INFO] Target genome list was writen to GCF_020162275.1_ASM2016227v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:51,413] [INFO] Task started: fastANI
[2024-01-24 15:10:51,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgff7e82ab-0a54-4dc4-b0f7-c0ebe8c6e37b/GCF_020162275.1_ASM2016227v1_genomic.fna.gz --refList GCF_020162275.1_ASM2016227v1_genomic.fna/target_genomes.txt --output GCF_020162275.1_ASM2016227v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:01,993] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:01,993] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:01,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:02,006] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:11:02,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:02,006] [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=DSM 2579	GCA_020162275.1	72	72	type	True	100.0	808	827	95	conclusive
Simonsiella muelleri	strain=ATCC 29453	GCA_002951835.1	72	72	type	True	99.9882	799	827	95	conclusive
Simonsiella muelleri	strain=ATCC 29453	GCA_000163775.2	72	72	type	True	99.9155	763	827	95	conclusive
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	80.475	271	827	95	below_threshold
Kingella kingae	strain=NCTC10529	GCA_900475905.1	504	504	type	True	80.4474	260	827	95	below_threshold
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	79.9721	447	827	95	below_threshold
Kingella kingae	strain=ATCC 23330	GCA_000213535.1	504	504	type	True	79.9275	264	827	95	below_threshold
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	79.8813	451	827	95	below_threshold
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	79.8564	421	827	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_020162295.1	194196	194196	type	True	79.4691	311	827	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_014054525.1	194196	194196	type	True	79.4193	322	827	95	below_threshold
Neisseria perflava	strain=CCUG 17915	GCA_023472875.1	33053	33053	suspected-type	True	77.8707	87	827	95	below_threshold
Neisseria cinerea	strain=CCUG 2156	GCA_021025975.1	483	483	type	True	77.8166	76	827	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	77.7857	78	827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,010] [INFO] DFAST Taxonomy check result was written to GCF_020162275.1_ASM2016227v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:02,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:02,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:02,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/checkm_data
[2024-01-24 15:11:02,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:02,039] [INFO] Task started: CheckM
[2024-01-24 15:11:02,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020162275.1_ASM2016227v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020162275.1_ASM2016227v1_genomic.fna/checkm_input GCF_020162275.1_ASM2016227v1_genomic.fna/checkm_result
[2024-01-24 15:11:32,428] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:32,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:32,449] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:32,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:32,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020162275.1_ASM2016227v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:32,450] [INFO] Task started: Blastn
[2024-01-24 15:11:32,450] [INFO] Running command: blastn -query GCF_020162275.1_ASM2016227v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b193a82-fe9a-40d6-807d-0fd6502743a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_020162275.1_ASM2016227v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:33,557] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:33,562] [INFO] Selected 8 target genomes.
[2024-01-24 15:11:33,562] [INFO] Target genome list was writen to GCF_020162275.1_ASM2016227v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:33,569] [INFO] Task started: fastANI
[2024-01-24 15:11:33,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgff7e82ab-0a54-4dc4-b0f7-c0ebe8c6e37b/GCF_020162275.1_ASM2016227v1_genomic.fna.gz --refList GCF_020162275.1_ASM2016227v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020162275.1_ASM2016227v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:39,342] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:39,351] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:39,351] [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	99.9883	803	827	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_900111845.1	s__Kingella kingae	80.1351	250	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	98.43	98.16	0.96	0.94	37	-
GCF_000745955.1	s__Alysiella crassa	79.8308	428	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	-
GCF_000751855.1	s__Kingella negevensis	79.5412	257	827	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	79.3771	330	827	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	77.5008	174	827	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	77.3023	77	827	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	77.2187	66	827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.5569	97.07	96.76	0.92	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:39,353] [INFO] GTDB search result was written to GCF_020162275.1_ASM2016227v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:39,354] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:39,358] [INFO] DFAST_QC result json was written to GCF_020162275.1_ASM2016227v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:39,359] [INFO] DFAST_QC completed!
[2024-01-24 15:11:39,359] [INFO] Total running time: 0h0m58s