[2024-01-24 12:53:57,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:57,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:57,084] [INFO] DQC Reference Directory: /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference
[2024-01-24 12:53:58,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:58,358] [INFO] Task started: Prodigal
[2024-01-24 12:53:58,358] [INFO] Running command: gunzip -c /var/lib/cwl/stg3831e95e-c6ac-40ed-b003-1df129620b1e/GCF_011516925.1_ASM1151692v1_genomic.fna.gz | prodigal -d GCF_011516925.1_ASM1151692v1_genomic.fna/cds.fna -a GCF_011516925.1_ASM1151692v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:08,627] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:08,627] [INFO] Task started: HMMsearch
[2024-01-24 12:54:08,628] [INFO] Running command: hmmsearch --tblout GCF_011516925.1_ASM1151692v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/reference_markers.hmm GCF_011516925.1_ASM1151692v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:08,890] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:08,892] [INFO] Found 6/6 markers.
[2024-01-24 12:54:08,923] [INFO] Query marker FASTA was written to GCF_011516925.1_ASM1151692v1_genomic.fna/markers.fasta
[2024-01-24 12:54:08,923] [INFO] Task started: Blastn
[2024-01-24 12:54:08,923] [INFO] Running command: blastn -query GCF_011516925.1_ASM1151692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/reference_markers.fasta -out GCF_011516925.1_ASM1151692v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:09,650] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:09,653] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:09,653] [INFO] Target genome list was writen to GCF_011516925.1_ASM1151692v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:09,658] [INFO] Task started: fastANI
[2024-01-24 12:54:09,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg3831e95e-c6ac-40ed-b003-1df129620b1e/GCF_011516925.1_ASM1151692v1_genomic.fna.gz --refList GCF_011516925.1_ASM1151692v1_genomic.fna/target_genomes.txt --output GCF_011516925.1_ASM1151692v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:18,243] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:18,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:18,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:18,254] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:18,254] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:18,254] [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	100.0	992	996	95	conclusive
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	93.6746	816	996	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	93.6483	815	996	95	below_threshold
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	87.9417	768	996	95	below_threshold
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	85.9455	701	996	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	85.7182	687	996	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	85.5333	701	996	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.6686	423	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:18,258] [INFO] DFAST Taxonomy check result was written to GCF_011516925.1_ASM1151692v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:18,258] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:18,258] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:18,259] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/checkm_data
[2024-01-24 12:54:18,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:18,297] [INFO] Task started: CheckM
[2024-01-24 12:54:18,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011516925.1_ASM1151692v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011516925.1_ASM1151692v1_genomic.fna/checkm_input GCF_011516925.1_ASM1151692v1_genomic.fna/checkm_result
[2024-01-24 12:54:50,279] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:50,280] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:50,299] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:50,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:50,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011516925.1_ASM1151692v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:50,300] [INFO] Task started: Blastn
[2024-01-24 12:54:50,300] [INFO] Running command: blastn -query GCF_011516925.1_ASM1151692v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg530c6e29-d203-4380-bffa-33e60af90728/dqc_reference/reference_markers_gtdb.fasta -out GCF_011516925.1_ASM1151692v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:51,373] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:51,377] [INFO] Selected 6 target genomes.
[2024-01-24 12:54:51,377] [INFO] Target genome list was writen to GCF_011516925.1_ASM1151692v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:51,385] [INFO] Task started: fastANI
[2024-01-24 12:54:51,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg3831e95e-c6ac-40ed-b003-1df129620b1e/GCF_011516925.1_ASM1151692v1_genomic.fna.gz --refList GCF_011516925.1_ASM1151692v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011516925.1_ASM1151692v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:55,683] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:55,691] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:55,691] [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	100.0	992	996	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	93.6548	815	996	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	87.9306	769	996	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	86.0187	661	996	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	85.9455	701	996	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	85.7177	687	996	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:55,693] [INFO] GTDB search result was written to GCF_011516925.1_ASM1151692v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:55,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:55,697] [INFO] DFAST_QC result json was written to GCF_011516925.1_ASM1151692v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:55,697] [INFO] DFAST_QC completed!
[2024-01-24 12:54:55,697] [INFO] Total running time: 0h0m59s