[2023-06-29 12:22:11,165] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:22:11,169] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:22:11,169] [INFO] DQC Reference Directory: /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference
[2023-06-29 12:22:12,539] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:22:12,539] [INFO] Task started: Prodigal
[2023-06-29 12:22:12,540] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6922727-0483-445b-8093-28a7469ddf3c/GCA_021637345.1_ASM2163734v1_genomic.fna.gz | prodigal -d GCA_021637345.1_ASM2163734v1_genomic.fna/cds.fna -a GCA_021637345.1_ASM2163734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:22:16,418] [INFO] Task succeeded: Prodigal
[2023-06-29 12:22:16,419] [INFO] Task started: HMMsearch
[2023-06-29 12:22:16,419] [INFO] Running command: hmmsearch --tblout GCA_021637345.1_ASM2163734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/reference_markers.hmm GCA_021637345.1_ASM2163734v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:22:16,688] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:22:16,689] [INFO] Found 6/6 markers.
[2023-06-29 12:22:16,726] [INFO] Query marker FASTA was written to GCA_021637345.1_ASM2163734v1_genomic.fna/markers.fasta
[2023-06-29 12:22:16,727] [INFO] Task started: Blastn
[2023-06-29 12:22:16,727] [INFO] Running command: blastn -query GCA_021637345.1_ASM2163734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/reference_markers.fasta -out GCA_021637345.1_ASM2163734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:17,463] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:17,467] [INFO] Selected 29 target genomes.
[2023-06-29 12:22:17,467] [INFO] Target genome list was writen to GCA_021637345.1_ASM2163734v1_genomic.fna/target_genomes.txt
[2023-06-29 12:22:17,478] [INFO] Task started: fastANI
[2023-06-29 12:22:17,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6922727-0483-445b-8093-28a7469ddf3c/GCA_021637345.1_ASM2163734v1_genomic.fna.gz --refList GCA_021637345.1_ASM2163734v1_genomic.fna/target_genomes.txt --output GCA_021637345.1_ASM2163734v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:22:31,896] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:31,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:22:31,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:22:31,905] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:22:31,905] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:22:31,905] [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
Succinivibrio dextrinosolvens	strain=DSM 3072	GCA_900167015.1	83771	83771	type	True	79.0104	206	750	95	below_threshold
Anaerobiospirillum succiniciproducens	strain=DSM 6400	GCA_000482845.1	13335	13335	type	True	77.1553	69	750	95	below_threshold
Anaerobiospirillum thomasii	strain=NCTC12467	GCA_900445255.1	179995	179995	type	True	76.8172	63	750	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:22:31,909] [INFO] DFAST Taxonomy check result was written to GCA_021637345.1_ASM2163734v1_genomic.fna/tc_result.tsv
[2023-06-29 12:22:31,910] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:22:31,910] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:22:31,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/checkm_data
[2023-06-29 12:22:31,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:22:31,944] [INFO] Task started: CheckM
[2023-06-29 12:22:31,945] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021637345.1_ASM2163734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021637345.1_ASM2163734v1_genomic.fna/checkm_input GCA_021637345.1_ASM2163734v1_genomic.fna/checkm_result
[2023-06-29 12:22:52,118] [INFO] Task succeeded: CheckM
[2023-06-29 12:22:52,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:22:52,144] [INFO] ===== Completeness check finished =====
[2023-06-29 12:22:52,144] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:22:52,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021637345.1_ASM2163734v1_genomic.fna/markers.fasta)
[2023-06-29 12:22:52,145] [INFO] Task started: Blastn
[2023-06-29 12:22:52,145] [INFO] Running command: blastn -query GCA_021637345.1_ASM2163734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf21cc075-985d-4ca2-8ff9-9f82c7388fa3/dqc_reference/reference_markers_gtdb.fasta -out GCA_021637345.1_ASM2163734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:22:53,120] [INFO] Task succeeded: Blastn
[2023-06-29 12:22:53,124] [INFO] Selected 10 target genomes.
[2023-06-29 12:22:53,124] [INFO] Target genome list was writen to GCA_021637345.1_ASM2163734v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:22:53,134] [INFO] Task started: fastANI
[2023-06-29 12:22:53,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6922727-0483-445b-8093-28a7469ddf3c/GCA_021637345.1_ASM2163734v1_genomic.fna.gz --refList GCA_021637345.1_ASM2163734v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021637345.1_ASM2163734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:22:57,937] [INFO] Task succeeded: fastANI
[2023-06-29 12:22:57,947] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:22:57,947] [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
GCA_000431835.1	s__Succinivibrio sp000431835	98.1171	637	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.12	95.78	0.87	0.82	11	conclusive
GCA_900315395.1	s__Succinivibrio sp900315395	90.0609	574	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.82	99.64	0.93	0.87	3	-
GCA_002449335.1	s__Succinivibrio sp002449335	89.7699	618	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.89	95.86	0.90	0.86	3	-
GCA_012519775.1	s__Succinivibrio sp012519775	79.888	236	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785325.1	s__Succinivibrio sp003456415	79.696	252	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.60	98.18	0.90	0.86	5	-
GCA_900316375.1	s__Succinivibrio sp900316375	79.6112	282	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.95	99.95	0.97	0.97	2	-
GCA_004556245.1	s__Succinivibrio hippei_B	79.396	166	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167015.1	s__Succinivibrio dextrinosolvens	79.0104	206	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	96.59	96.11	0.85	0.83	6	-
GCF_011065405.1	s__Succinivibrio dextrinosolvens_A	78.8653	186	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.30	97.32	0.93	0.84	6	-
GCA_900317105.1	s__Succinivibrio sp900317105	78.5516	164	750	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.54	96.63	0.90	0.79	4	-
--------------------------------------------------------------------------------
[2023-06-29 12:22:57,949] [INFO] GTDB search result was written to GCA_021637345.1_ASM2163734v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:22:57,950] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:22:57,953] [INFO] DFAST_QC result json was written to GCA_021637345.1_ASM2163734v1_genomic.fna/dqc_result.json
[2023-06-29 12:22:57,953] [INFO] DFAST_QC completed!
[2023-06-29 12:22:57,953] [INFO] Total running time: 0h0m47s