[2024-01-25 20:27:35,725] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:27:35,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:27:35,727] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference
[2024-01-25 20:27:36,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:27:36,918] [INFO] Task started: Prodigal
[2024-01-25 20:27:36,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c3bc37d-d72a-465a-8203-c01dc3d5a07f/GCF_025995655.1_ASM2599565v1_genomic.fna.gz | prodigal -d GCF_025995655.1_ASM2599565v1_genomic.fna/cds.fna -a GCF_025995655.1_ASM2599565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:27:47,132] [INFO] Task succeeded: Prodigal
[2024-01-25 20:27:47,132] [INFO] Task started: HMMsearch
[2024-01-25 20:27:47,132] [INFO] Running command: hmmsearch --tblout GCF_025995655.1_ASM2599565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/reference_markers.hmm GCF_025995655.1_ASM2599565v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:27:47,364] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:27:47,365] [INFO] Found 6/6 markers.
[2024-01-25 20:27:47,395] [INFO] Query marker FASTA was written to GCF_025995655.1_ASM2599565v1_genomic.fna/markers.fasta
[2024-01-25 20:27:47,395] [INFO] Task started: Blastn
[2024-01-25 20:27:47,396] [INFO] Running command: blastn -query GCF_025995655.1_ASM2599565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/reference_markers.fasta -out GCF_025995655.1_ASM2599565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:27:48,022] [INFO] Task succeeded: Blastn
[2024-01-25 20:27:48,025] [INFO] Selected 21 target genomes.
[2024-01-25 20:27:48,026] [INFO] Target genome list was writen to GCF_025995655.1_ASM2599565v1_genomic.fna/target_genomes.txt
[2024-01-25 20:27:48,045] [INFO] Task started: fastANI
[2024-01-25 20:27:48,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c3bc37d-d72a-465a-8203-c01dc3d5a07f/GCF_025995655.1_ASM2599565v1_genomic.fna.gz --refList GCF_025995655.1_ASM2599565v1_genomic.fna/target_genomes.txt --output GCF_025995655.1_ASM2599565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:28:02,344] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:02,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:28:02,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:28:02,353] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:28:02,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:28:02,353] [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 malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	99.9814	1232	1256	95	conclusive
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	93.2204	826	1256	95	below_threshold
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	86.2053	749	1256	95	below_threshold
Acetobacter orleanensis	strain=NBRC 13752	GCA_006539325.1	104099	104099	type	True	85.3089	694	1256	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	85.3047	695	1256	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	85.209	707	1256	95	below_threshold
Acetobacter oryzifermentans	strain=SLV-7	GCA_001628715.1	1633874	1633874	type	True	78.6451	330	1256	95	below_threshold
Acetobacter orientalis	strain=21F-2	GCA_000963965.1	146474	146474	type	True	78.5601	295	1256	95	below_threshold
Acetobacter orientalis	strain=NBRC 16606	GCA_007989335.1	146474	146474	type	True	78.5527	294	1256	95	below_threshold
Acetobacter oeni	strain=DSM 23926	GCA_014196315.1	304077	304077	type	True	77.1535	118	1256	95	below_threshold
Acetobacter oeni	strain=LMG 21952	GCA_011516825.1	304077	304077	type	True	77.1211	120	1256	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.9686	57	1256	95	below_threshold
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	75.9481	64	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:28:02,354] [INFO] DFAST Taxonomy check result was written to GCF_025995655.1_ASM2599565v1_genomic.fna/tc_result.tsv
[2024-01-25 20:28:02,355] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:28:02,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:28:02,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/checkm_data
[2024-01-25 20:28:02,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:28:02,393] [INFO] Task started: CheckM
[2024-01-25 20:28:02,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995655.1_ASM2599565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995655.1_ASM2599565v1_genomic.fna/checkm_input GCF_025995655.1_ASM2599565v1_genomic.fna/checkm_result
[2024-01-25 20:28:34,479] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:34,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:34,496] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:34,496] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:34,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995655.1_ASM2599565v1_genomic.fna/markers.fasta)
[2024-01-25 20:28:34,497] [INFO] Task started: Blastn
[2024-01-25 20:28:34,497] [INFO] Running command: blastn -query GCF_025995655.1_ASM2599565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d0dff2-69bc-4ee2-9843-d3e219d24d09/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995655.1_ASM2599565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:35,407] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:35,414] [INFO] Selected 15 target genomes.
[2024-01-25 20:28:35,414] [INFO] Target genome list was writen to GCF_025995655.1_ASM2599565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:35,442] [INFO] Task started: fastANI
[2024-01-25 20:28:35,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c3bc37d-d72a-465a-8203-c01dc3d5a07f/GCF_025995655.1_ASM2599565v1_genomic.fna.gz --refList GCF_025995655.1_ASM2599565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995655.1_ASM2599565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:45,389] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:45,397] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:45,397] [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_001580615.1	s__Acetobacter malorum	99.9814	1232	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	conclusive
GCF_001580535.1	s__Acetobacter cerevisiae	93.2086	827	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_002153605.1	s__Acetobacter malorum_A	90.9051	810	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_000613905.1	s__Acetobacter persici	86.2078	749	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001581005.1	s__Acetobacter orleanensis	85.209	707	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_011516935.1	s__Acetobacter farinalis	84.0143	681	1256	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	78.7126	324	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001628715.1	s__Acetobacter oryzifermentans	78.6507	329	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	98.04	0.87	0.83	24	-
GCF_006538165.1	s__Komagataeibacter diospyri	77.4353	206	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_011516825.1	s__Acetobacter oeni	77.1197	119	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000687875.1	s__Acidocella facilis	75.9351	63	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:28:45,398] [INFO] GTDB search result was written to GCF_025995655.1_ASM2599565v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:45,399] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:45,401] [INFO] DFAST_QC result json was written to GCF_025995655.1_ASM2599565v1_genomic.fna/dqc_result.json
[2024-01-25 20:28:45,402] [INFO] DFAST_QC completed!
[2024-01-25 20:28:45,402] [INFO] Total running time: 0h1m10s