[2024-01-25 19:08:50,502] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:50,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:50,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference
[2024-01-25 19:08:51,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:51,631] [INFO] Task started: Prodigal
[2024-01-25 19:08:51,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg616564d5-5c2b-44e7-8553-98a954a36d02/GCF_002111595.1_ASM211159v1_genomic.fna.gz | prodigal -d GCF_002111595.1_ASM211159v1_genomic.fna/cds.fna -a GCF_002111595.1_ASM211159v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:00,685] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:00,685] [INFO] Task started: HMMsearch
[2024-01-25 19:09:00,685] [INFO] Running command: hmmsearch --tblout GCF_002111595.1_ASM211159v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/reference_markers.hmm GCF_002111595.1_ASM211159v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:00,895] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:00,897] [INFO] Found 6/6 markers.
[2024-01-25 19:09:00,929] [INFO] Query marker FASTA was written to GCF_002111595.1_ASM211159v1_genomic.fna/markers.fasta
[2024-01-25 19:09:00,929] [INFO] Task started: Blastn
[2024-01-25 19:09:00,929] [INFO] Running command: blastn -query GCF_002111595.1_ASM211159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/reference_markers.fasta -out GCF_002111595.1_ASM211159v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:01,769] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:01,773] [INFO] Selected 14 target genomes.
[2024-01-25 19:09:01,773] [INFO] Target genome list was writen to GCF_002111595.1_ASM211159v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:01,785] [INFO] Task started: fastANI
[2024-01-25 19:09:01,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg616564d5-5c2b-44e7-8553-98a954a36d02/GCF_002111595.1_ASM211159v1_genomic.fna.gz --refList GCF_002111595.1_ASM211159v1_genomic.fna/target_genomes.txt --output GCF_002111595.1_ASM211159v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:13,656] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:13,657] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:13,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:13,667] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:13,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:13,667] [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
Lonsdalea britannica	strain=LMG 26267	GCA_002111595.1	1082704	1082704	type	True	100.0	1267	1269	95	conclusive
Lonsdalea iberica	strain=LMG 26264	GCA_002111585.1	1082703	1082703	type	True	89.8088	1078	1269	95	below_threshold
Lonsdalea quercina	strain=ATCC 29281	GCA_900107885.1	71657	71657	type	True	89.0126	1084	1269	95	below_threshold
Lonsdalea quercina subsp. quercina	strain=ATCC 29281	GCA_000688655.1	1082705	71657	type	True	88.9773	1113	1269	95	below_threshold
Dickeya fangzhongdai	strain=CGMCC 1.15464	GCA_014642955.1	1778540	1778540	type	True	79.8456	581	1269	95	below_threshold
Dickeya dadantii subsp. dieffenbachiae	strain=NCPPB 2976	GCA_000406185.1	204040	204038	type	True	79.7096	573	1269	95	below_threshold
Dickeya parazeae	strain=S31	GCA_017897605.1	2893572	2893572	type	True	79.2957	453	1269	95	below_threshold
Pectobacterium colocasium	strain=LJ1	GCA_020181655.1	2878098	2878098	type	True	79.0837	429	1269	95	below_threshold
Brenneria roseae subsp. roseae	strain=LMG 27714	GCA_003115845.1	1508506	1509241	type	True	79.0582	439	1269	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.9165	423	1269	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	78.8642	429	1269	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	78.7628	452	1269	95	below_threshold
Cronobacter muytjensii	strain=ATCC 51329	GCA_000409285.1	413501	413501	type	True	78.5485	326	1269	95	below_threshold
Cronobacter sakazakii	strain=ATCC 29544	GCA_001971035.1	28141	28141	type	True	78.2111	318	1269	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:13,669] [INFO] DFAST Taxonomy check result was written to GCF_002111595.1_ASM211159v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:13,669] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:13,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:13,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/checkm_data
[2024-01-25 19:09:13,670] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:13,709] [INFO] Task started: CheckM
[2024-01-25 19:09:13,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002111595.1_ASM211159v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002111595.1_ASM211159v1_genomic.fna/checkm_input GCF_002111595.1_ASM211159v1_genomic.fna/checkm_result
[2024-01-25 19:09:43,680] [INFO] Task succeeded: CheckM
[2024-01-25 19:09:43,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:09:43,699] [INFO] ===== Completeness check finished =====
[2024-01-25 19:09:43,699] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:09:43,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002111595.1_ASM211159v1_genomic.fna/markers.fasta)
[2024-01-25 19:09:43,699] [INFO] Task started: Blastn
[2024-01-25 19:09:43,699] [INFO] Running command: blastn -query GCF_002111595.1_ASM211159v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101a98db-a028-4909-bf8c-9b4232063874/dqc_reference/reference_markers_gtdb.fasta -out GCF_002111595.1_ASM211159v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:45,049] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:45,052] [INFO] Selected 5 target genomes.
[2024-01-25 19:09:45,052] [INFO] Target genome list was writen to GCF_002111595.1_ASM211159v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:09:45,058] [INFO] Task started: fastANI
[2024-01-25 19:09:45,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg616564d5-5c2b-44e7-8553-98a954a36d02/GCF_002111595.1_ASM211159v1_genomic.fna.gz --refList GCF_002111595.1_ASM211159v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002111595.1_ASM211159v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:50,439] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:50,443] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:50,444] [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_002111595.1	s__Lonsdalea britannica	100.0	1267	1269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.31	98.65	0.97	0.93	3	conclusive
GCF_015999465.1	s__Lonsdalea populi	90.2491	1057	1269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.60	99.19	0.97	0.95	28	-
GCF_002111585.1	s__Lonsdalea iberica	89.8067	1079	1269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	98.99	98.99	0.92	0.92	2	-
GCF_000688695.1	s__Lonsdalea quercina_D	89.7206	1129	1269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.95	99.95	0.99	0.99	2	-
GCF_000688655.1	s__Lonsdalea quercina	88.9773	1113	1269	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Lonsdalea	95.0	99.93	99.93	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:50,445] [INFO] GTDB search result was written to GCF_002111595.1_ASM211159v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:50,445] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:50,448] [INFO] DFAST_QC result json was written to GCF_002111595.1_ASM211159v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:50,448] [INFO] DFAST_QC completed!
[2024-01-25 19:09:50,448] [INFO] Total running time: 0h0m60s