[2023-06-13 02:32:35,544] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:35,556] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:35,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference
[2023-06-13 02:32:36,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:36,838] [INFO] Task started: Prodigal
[2023-06-13 02:32:36,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg606a6136-92ce-44d5-b903-833fe201e2be/GCA_022483405.1_ASM2248340v1_genomic.fna.gz | prodigal -d GCA_022483405.1_ASM2248340v1_genomic.fna/cds.fna -a GCA_022483405.1_ASM2248340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:46,867] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:46,867] [INFO] Task started: HMMsearch
[2023-06-13 02:32:46,867] [INFO] Running command: hmmsearch --tblout GCA_022483405.1_ASM2248340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/reference_markers.hmm GCA_022483405.1_ASM2248340v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:47,144] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:47,146] [INFO] Found 6/6 markers.
[2023-06-13 02:32:47,182] [INFO] Query marker FASTA was written to GCA_022483405.1_ASM2248340v1_genomic.fna/markers.fasta
[2023-06-13 02:32:47,183] [INFO] Task started: Blastn
[2023-06-13 02:32:47,183] [INFO] Running command: blastn -query GCA_022483405.1_ASM2248340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/reference_markers.fasta -out GCA_022483405.1_ASM2248340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:47,898] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:47,902] [INFO] Selected 11 target genomes.
[2023-06-13 02:32:47,902] [INFO] Target genome list was writen to GCA_022483405.1_ASM2248340v1_genomic.fna/target_genomes.txt
[2023-06-13 02:32:47,904] [INFO] Task started: fastANI
[2023-06-13 02:32:47,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg606a6136-92ce-44d5-b903-833fe201e2be/GCA_022483405.1_ASM2248340v1_genomic.fna.gz --refList GCA_022483405.1_ASM2248340v1_genomic.fna/target_genomes.txt --output GCA_022483405.1_ASM2248340v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:32:55,315] [INFO] Task succeeded: fastANI
[2023-06-13 02:32:55,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:32:55,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:32:55,326] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 02:32:55,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 02:32:55,326] [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
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	97.9259	832	965	95	conclusive
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	93.7148	813	965	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	93.6816	812	965	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	87.679	758	965	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	85.6855	667	965	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	85.5762	682	965	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	85.2907	682	965	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.7183	422	965	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:32:55,329] [INFO] DFAST Taxonomy check result was written to GCA_022483405.1_ASM2248340v1_genomic.fna/tc_result.tsv
[2023-06-13 02:32:55,329] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:32:55,330] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:32:55,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/checkm_data
[2023-06-13 02:32:55,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:32:55,363] [INFO] Task started: CheckM
[2023-06-13 02:32:55,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022483405.1_ASM2248340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022483405.1_ASM2248340v1_genomic.fna/checkm_input GCA_022483405.1_ASM2248340v1_genomic.fna/checkm_result
[2023-06-13 02:33:28,129] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:28,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:28,159] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:28,160] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:28,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022483405.1_ASM2248340v1_genomic.fna/markers.fasta)
[2023-06-13 02:33:28,161] [INFO] Task started: Blastn
[2023-06-13 02:33:28,161] [INFO] Running command: blastn -query GCA_022483405.1_ASM2248340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cc7863-15f8-4dad-967e-e61699e78412/dqc_reference/reference_markers_gtdb.fasta -out GCA_022483405.1_ASM2248340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:29,281] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:29,290] [INFO] Selected 6 target genomes.
[2023-06-13 02:33:29,290] [INFO] Target genome list was writen to GCA_022483405.1_ASM2248340v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:29,293] [INFO] Task started: fastANI
[2023-06-13 02:33:29,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg606a6136-92ce-44d5-b903-833fe201e2be/GCA_022483405.1_ASM2248340v1_genomic.fna.gz --refList GCA_022483405.1_ASM2248340v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022483405.1_ASM2248340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:33,910] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:33,920] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:33:33,921] [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_011516925.1	s__Acetobacter fabarum	97.9513	831	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	conclusive
GCF_014207635.1	s__Acetobacter lovaniensis	93.7377	809	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011516885.1	s__Acetobacter lambici	87.679	758	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002153655.1	s__Acetobacter okinawensis_A	86.0374	658	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	85.6836	668	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_001499675.1	s__Acetobacter ghanensis	85.5371	681	965	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:33,923] [INFO] GTDB search result was written to GCA_022483405.1_ASM2248340v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:33,923] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:33,926] [INFO] DFAST_QC result json was written to GCA_022483405.1_ASM2248340v1_genomic.fna/dqc_result.json
[2023-06-13 02:33:33,926] [INFO] DFAST_QC completed!
[2023-06-13 02:33:33,927] [INFO] Total running time: 0h0m58s