[2023-06-13 11:39:22,290] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:39:22,293] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:39:22,293] [INFO] DQC Reference Directory: /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference
[2023-06-13 11:39:23,475] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:39:23,476] [INFO] Task started: Prodigal
[2023-06-13 11:39:23,476] [INFO] Running command: gunzip -c /var/lib/cwl/stg145971cb-dad4-484c-a5b5-9658930504a8/GCA_022646825.1_ASM2264682v1_genomic.fna.gz | prodigal -d GCA_022646825.1_ASM2264682v1_genomic.fna/cds.fna -a GCA_022646825.1_ASM2264682v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:39:30,964] [INFO] Task succeeded: Prodigal
[2023-06-13 11:39:30,964] [INFO] Task started: HMMsearch
[2023-06-13 11:39:30,964] [INFO] Running command: hmmsearch --tblout GCA_022646825.1_ASM2264682v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/reference_markers.hmm GCA_022646825.1_ASM2264682v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:39:31,223] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:39:31,225] [INFO] Found 6/6 markers.
[2023-06-13 11:39:31,255] [INFO] Query marker FASTA was written to GCA_022646825.1_ASM2264682v1_genomic.fna/markers.fasta
[2023-06-13 11:39:31,255] [INFO] Task started: Blastn
[2023-06-13 11:39:31,255] [INFO] Running command: blastn -query GCA_022646825.1_ASM2264682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/reference_markers.fasta -out GCA_022646825.1_ASM2264682v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:39:31,947] [INFO] Task succeeded: Blastn
[2023-06-13 11:39:31,951] [INFO] Selected 11 target genomes.
[2023-06-13 11:39:31,951] [INFO] Target genome list was writen to GCA_022646825.1_ASM2264682v1_genomic.fna/target_genomes.txt
[2023-06-13 11:39:31,955] [INFO] Task started: fastANI
[2023-06-13 11:39:31,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg145971cb-dad4-484c-a5b5-9658930504a8/GCA_022646825.1_ASM2264682v1_genomic.fna.gz --refList GCA_022646825.1_ASM2264682v1_genomic.fna/target_genomes.txt --output GCA_022646825.1_ASM2264682v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:39:38,823] [INFO] Task succeeded: fastANI
[2023-06-13 11:39:38,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:39:38,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:39:38,843] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 11:39:38,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 11:39:38,843] [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	98.2438	697	725	95	conclusive
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	94.3711	689	725	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	94.3707	687	725	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	88.1342	664	725	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	86.0409	589	725	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	85.7615	603	725	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	85.6846	611	725	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.2123	392	725	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:39:38,847] [INFO] DFAST Taxonomy check result was written to GCA_022646825.1_ASM2264682v1_genomic.fna/tc_result.tsv
[2023-06-13 11:39:38,848] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:39:38,848] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:39:38,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/checkm_data
[2023-06-13 11:39:38,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:39:38,876] [INFO] Task started: CheckM
[2023-06-13 11:39:38,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022646825.1_ASM2264682v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022646825.1_ASM2264682v1_genomic.fna/checkm_input GCA_022646825.1_ASM2264682v1_genomic.fna/checkm_result
[2023-06-13 11:40:05,528] [INFO] Task succeeded: CheckM
[2023-06-13 11:40:05,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:40:05,551] [INFO] ===== Completeness check finished =====
[2023-06-13 11:40:05,551] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:40:05,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022646825.1_ASM2264682v1_genomic.fna/markers.fasta)
[2023-06-13 11:40:05,552] [INFO] Task started: Blastn
[2023-06-13 11:40:05,552] [INFO] Running command: blastn -query GCA_022646825.1_ASM2264682v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg811513af-1646-4126-a7e9-a6d86fb22731/dqc_reference/reference_markers_gtdb.fasta -out GCA_022646825.1_ASM2264682v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:40:06,718] [INFO] Task succeeded: Blastn
[2023-06-13 11:40:06,723] [INFO] Selected 6 target genomes.
[2023-06-13 11:40:06,723] [INFO] Target genome list was writen to GCA_022646825.1_ASM2264682v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:40:06,727] [INFO] Task started: fastANI
[2023-06-13 11:40:06,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg145971cb-dad4-484c-a5b5-9658930504a8/GCA_022646825.1_ASM2264682v1_genomic.fna.gz --refList GCA_022646825.1_ASM2264682v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022646825.1_ASM2264682v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:40:10,952] [INFO] Task succeeded: fastANI
[2023-06-13 11:40:10,961] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:40:10,962] [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	98.2438	697	725	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	94.3706	687	725	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	88.1342	664	725	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	86.4604	599	725	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	86.0409	589	725	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	85.7381	604	725	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 11:40:10,964] [INFO] GTDB search result was written to GCA_022646825.1_ASM2264682v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:40:10,965] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:40:10,970] [INFO] DFAST_QC result json was written to GCA_022646825.1_ASM2264682v1_genomic.fna/dqc_result.json
[2023-06-13 11:40:10,970] [INFO] DFAST_QC completed!
[2023-06-13 11:40:10,970] [INFO] Total running time: 0h0m49s