[2024-01-25 17:46:50,468] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:50,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:50,471] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference
[2024-01-25 17:46:51,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:51,724] [INFO] Task started: Prodigal
[2024-01-25 17:46:51,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg5dc9f1b3-81fa-4833-8944-97f61c3f3f55/GCF_022871045.1_ASM2287104v1_genomic.fna.gz | prodigal -d GCF_022871045.1_ASM2287104v1_genomic.fna/cds.fna -a GCF_022871045.1_ASM2287104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:01,285] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:01,286] [INFO] Task started: HMMsearch
[2024-01-25 17:47:01,286] [INFO] Running command: hmmsearch --tblout GCF_022871045.1_ASM2287104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/reference_markers.hmm GCF_022871045.1_ASM2287104v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:01,503] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:01,504] [INFO] Found 6/6 markers.
[2024-01-25 17:47:01,529] [INFO] Query marker FASTA was written to GCF_022871045.1_ASM2287104v1_genomic.fna/markers.fasta
[2024-01-25 17:47:01,529] [INFO] Task started: Blastn
[2024-01-25 17:47:01,530] [INFO] Running command: blastn -query GCF_022871045.1_ASM2287104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/reference_markers.fasta -out GCF_022871045.1_ASM2287104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:02,134] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:02,137] [INFO] Selected 11 target genomes.
[2024-01-25 17:47:02,138] [INFO] Target genome list was writen to GCF_022871045.1_ASM2287104v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:02,147] [INFO] Task started: fastANI
[2024-01-25 17:47:02,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc9f1b3-81fa-4833-8944-97f61c3f3f55/GCF_022871045.1_ASM2287104v1_genomic.fna.gz --refList GCF_022871045.1_ASM2287104v1_genomic.fna/target_genomes.txt --output GCF_022871045.1_ASM2287104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:18,173] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:18,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:18,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:18,181] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:47:18,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:18,182] [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
Alysiella crassa	strain=S6	GCA_022871045.1	153491	153491	type	True	100.0	968	969	95	conclusive
Alysiella crassa	strain=NCTC10283	GCA_900445245.1	153491	153491	type	True	99.9676	935	969	95	conclusive
Alysiella crassa	strain=DSM 2578	GCA_000745955.1	153491	153491	type	True	99.8035	828	969	95	conclusive
Alysiella filiformis	strain=DSM 16848	GCA_020162295.1	194196	194196	type	True	85.6658	509	969	95	below_threshold
Alysiella filiformis	strain=DSM 16848	GCA_014054525.1	194196	194196	type	True	85.6123	503	969	95	below_threshold
Simonsiella muelleri	strain=ATCC 29453	GCA_002951835.1	72	72	type	True	79.9884	442	969	95	below_threshold
Kingella kingae	strain=4177/66	GCA_022871005.1	504	504	type	True	79.8908	354	969	95	below_threshold
Simonsiella muelleri	strain=ATCC 29453	GCA_000163775.2	72	72	type	True	79.8735	438	969	95	below_threshold
Uruburuella suis	strain=1258/02	GCA_022870845.1	252130	252130	type	True	77.8383	147	969	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	77.6671	137	969	95	below_threshold
Uruburuella suis	strain=DSM 17474	GCA_004341385.1	252130	252130	type	True	77.033	137	969	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:18,183] [INFO] DFAST Taxonomy check result was written to GCF_022871045.1_ASM2287104v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:18,184] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:18,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:18,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/checkm_data
[2024-01-25 17:47:18,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:18,220] [INFO] Task started: CheckM
[2024-01-25 17:47:18,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022871045.1_ASM2287104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022871045.1_ASM2287104v1_genomic.fna/checkm_input GCF_022871045.1_ASM2287104v1_genomic.fna/checkm_result
[2024-01-25 17:47:50,787] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:50,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:50,809] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:50,809] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:50,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022871045.1_ASM2287104v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:50,810] [INFO] Task started: Blastn
[2024-01-25 17:47:50,810] [INFO] Running command: blastn -query GCF_022871045.1_ASM2287104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa4d78a9-b9e8-462a-b253-e70e6c59c9dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_022871045.1_ASM2287104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:51,899] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:51,902] [INFO] Selected 10 target genomes.
[2024-01-25 17:47:51,902] [INFO] Target genome list was writen to GCF_022871045.1_ASM2287104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:51,911] [INFO] Task started: fastANI
[2024-01-25 17:47:51,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg5dc9f1b3-81fa-4833-8944-97f61c3f3f55/GCF_022871045.1_ASM2287104v1_genomic.fna.gz --refList GCF_022871045.1_ASM2287104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022871045.1_ASM2287104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:01,189] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:01,196] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:01,196] [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_000745955.1	s__Alysiella crassa	99.8035	828	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.94	99.94	0.99	0.99	2	conclusive
GCF_014054525.1	s__Alysiella filiformis	85.7621	498	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Alysiella	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002951835.1	s__Simonsiella muelleri	80.0224	446	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Simonsiella	95.0	99.93	99.93	0.98	0.98	2	-
GCF_900111845.1	s__Kingella kingae	79.4794	341	969	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	79.2814	330	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella	95.0	99.09	98.48	0.96	0.94	3	-
GCF_014054725.1	s__Conchiformibius steedae	78.5582	273	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	98.09	96.18	0.94	0.87	3	-
GCF_014054985.1	s__Kingella_B oralis	78.2314	297	969	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_000428785.1	s__Conchiformibius kuhniae	78.1329	258	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Conchiformibius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373195.1	s__Kingella_B oralis_A	77.7834	170	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Kingella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000220865.1	s__Neisseria macacae	77.2303	123	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Neisseria	96.509	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:01,197] [INFO] GTDB search result was written to GCF_022871045.1_ASM2287104v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:01,198] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:01,201] [INFO] DFAST_QC result json was written to GCF_022871045.1_ASM2287104v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:01,201] [INFO] DFAST_QC completed!
[2024-01-25 17:48:01,201] [INFO] Total running time: 0h1m11s