[2024-01-24 11:51:22,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:22,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:22,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference
[2024-01-24 11:51:23,916] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:23,917] [INFO] Task started: Prodigal
[2024-01-24 11:51:23,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgec5525a3-20e4-485e-844e-5c86b5a48c67/GCF_000787635.2_ASM78763v2_genomic.fna.gz | prodigal -d GCF_000787635.2_ASM78763v2_genomic.fna/cds.fna -a GCF_000787635.2_ASM78763v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:34,519] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:34,519] [INFO] Task started: HMMsearch
[2024-01-24 11:51:34,519] [INFO] Running command: hmmsearch --tblout GCF_000787635.2_ASM78763v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/reference_markers.hmm GCF_000787635.2_ASM78763v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:34,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:34,790] [INFO] Found 6/6 markers.
[2024-01-24 11:51:34,822] [INFO] Query marker FASTA was written to GCF_000787635.2_ASM78763v2_genomic.fna/markers.fasta
[2024-01-24 11:51:34,822] [INFO] Task started: Blastn
[2024-01-24 11:51:34,823] [INFO] Running command: blastn -query GCF_000787635.2_ASM78763v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/reference_markers.fasta -out GCF_000787635.2_ASM78763v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,578] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,590] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:35,590] [INFO] Target genome list was writen to GCF_000787635.2_ASM78763v2_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,595] [INFO] Task started: fastANI
[2024-01-24 11:51:35,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5525a3-20e4-485e-844e-5c86b5a48c67/GCF_000787635.2_ASM78763v2_genomic.fna.gz --refList GCF_000787635.2_ASM78763v2_genomic.fna/target_genomes.txt --output GCF_000787635.2_ASM78763v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:45,149] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:45,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:45,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:45,162] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:51:45,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:45,162] [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 tropicalis	strain=NBRC 16470	GCA_000787635.2	104102	104102	type	True	99.9999	1117	1131	95	conclusive
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	99.936	1066	1131	95	conclusive
Acetobacter tropicalis	strain=LMG 19825	GCA_001580915.1	104102	104102	type	True	99.9117	1057	1131	95	conclusive
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	92.0583	845	1131	95	below_threshold
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	81.4734	628	1131	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	81.1933	511	1131	95	below_threshold
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	80.8503	481	1131	95	below_threshold
Acetobacter oryzoeni	strain=B6	GCA_004014775.2	2500548	2500548	type	True	79.6096	366	1131	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:45,165] [INFO] DFAST Taxonomy check result was written to GCF_000787635.2_ASM78763v2_genomic.fna/tc_result.tsv
[2024-01-24 11:51:45,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:45,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:45,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/checkm_data
[2024-01-24 11:51:45,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:45,204] [INFO] Task started: CheckM
[2024-01-24 11:51:45,204] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000787635.2_ASM78763v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000787635.2_ASM78763v2_genomic.fna/checkm_input GCF_000787635.2_ASM78763v2_genomic.fna/checkm_result
[2024-01-24 11:52:21,232] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:21,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:21,259] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:21,259] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:21,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000787635.2_ASM78763v2_genomic.fna/markers.fasta)
[2024-01-24 11:52:21,260] [INFO] Task started: Blastn
[2024-01-24 11:52:21,261] [INFO] Running command: blastn -query GCF_000787635.2_ASM78763v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a69b07c-374d-445e-9ad8-ca53a7a789b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_000787635.2_ASM78763v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:22,556] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:22,561] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:22,561] [INFO] Target genome list was writen to GCF_000787635.2_ASM78763v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:22,571] [INFO] Task started: fastANI
[2024-01-24 11:52:22,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgec5525a3-20e4-485e-844e-5c86b5a48c67/GCF_000787635.2_ASM78763v2_genomic.fna.gz --refList GCF_000787635.2_ASM78763v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000787635.2_ASM78763v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:30,582] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:30,594] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:30,595] [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_001580915.1	s__Acetobacter tropicalis	99.9117	1057	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	conclusive
GCF_001580995.1	s__Acetobacter senegalensis	92.0522	845	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_000963945.1	s__Acetobacter indonesiensis	81.4835	617	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	-
GCF_001580535.1	s__Acetobacter cerevisiae	81.1803	512	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_000613905.1	s__Acetobacter persici	80.8497	481	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_002153605.1	s__Acetobacter malorum_A	80.5408	496	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_001580615.1	s__Acetobacter malorum	80.4563	519	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_011516935.1	s__Acetobacter farinalis	80.3192	497	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001581005.1	s__Acetobacter orleanensis	79.9199	462	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_004014775.2	s__Acetobacter oryzoeni	79.6128	366	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.72	97.29	0.89	0.84	4	-
GCF_011516885.1	s__Acetobacter lambici	79.5576	333	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723785.2	s__Acetobacter pasteurianus	79.1831	377	1131	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.11	97.27	0.89	0.78	27	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:30,596] [INFO] GTDB search result was written to GCF_000787635.2_ASM78763v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:30,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:30,602] [INFO] DFAST_QC result json was written to GCF_000787635.2_ASM78763v2_genomic.fna/dqc_result.json
[2024-01-24 11:52:30,602] [INFO] DFAST_QC completed!
[2024-01-24 11:52:30,602] [INFO] Total running time: 0h1m8s