[2024-01-24 10:57:37,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:37,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:37,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference
[2024-01-24 10:57:39,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:39,342] [INFO] Task started: Prodigal
[2024-01-24 10:57:39,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg63b80697-02c1-4f9b-9baf-3f34ee312d45/GCF_900445255.1_51485_H01_genomic.fna.gz | prodigal -d GCF_900445255.1_51485_H01_genomic.fna/cds.fna -a GCF_900445255.1_51485_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:45,703] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:45,704] [INFO] Task started: HMMsearch
[2024-01-24 10:57:45,704] [INFO] Running command: hmmsearch --tblout GCF_900445255.1_51485_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/reference_markers.hmm GCF_900445255.1_51485_H01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:45,964] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:45,966] [INFO] Found 6/6 markers.
[2024-01-24 10:57:45,994] [INFO] Query marker FASTA was written to GCF_900445255.1_51485_H01_genomic.fna/markers.fasta
[2024-01-24 10:57:45,995] [INFO] Task started: Blastn
[2024-01-24 10:57:45,995] [INFO] Running command: blastn -query GCF_900445255.1_51485_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/reference_markers.fasta -out GCF_900445255.1_51485_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:46,645] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:46,648] [INFO] Selected 20 target genomes.
[2024-01-24 10:57:46,649] [INFO] Target genome list was writen to GCF_900445255.1_51485_H01_genomic.fna/target_genomes.txt
[2024-01-24 10:57:46,761] [INFO] Task started: fastANI
[2024-01-24 10:57:46,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b80697-02c1-4f9b-9baf-3f34ee312d45/GCF_900445255.1_51485_H01_genomic.fna.gz --refList GCF_900445255.1_51485_H01_genomic.fna/target_genomes.txt --output GCF_900445255.1_51485_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:59,075] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:59,076] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:59,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:59,086] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:59,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:59,086] [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
Anaerobiospirillum thomasii	strain=NCTC12467	GCA_900445255.1	179995	179995	type	True	100.0	981	996	95	conclusive
Anaerobiospirillum succiniciproducens	strain=DSM 6400	GCA_000482845.1	13335	13335	type	True	77.3962	92	996	95	below_threshold
Succinatimonas hippei	strain=YIT 12066	GCA_000188195.1	626938	626938	type	True	77.2462	57	996	95	below_threshold
Succinivibrio dextrinosolvens	strain=DSM 3072	GCA_900167015.1	83771	83771	type	True	77.2199	62	996	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:59,089] [INFO] DFAST Taxonomy check result was written to GCF_900445255.1_51485_H01_genomic.fna/tc_result.tsv
[2024-01-24 10:57:59,090] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:59,090] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:59,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/checkm_data
[2024-01-24 10:57:59,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:59,130] [INFO] Task started: CheckM
[2024-01-24 10:57:59,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445255.1_51485_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445255.1_51485_H01_genomic.fna/checkm_input GCF_900445255.1_51485_H01_genomic.fna/checkm_result
[2024-01-24 10:58:24,856] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:24,857] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:24,884] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:24,885] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:24,885] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445255.1_51485_H01_genomic.fna/markers.fasta)
[2024-01-24 10:58:24,886] [INFO] Task started: Blastn
[2024-01-24 10:58:24,886] [INFO] Running command: blastn -query GCF_900445255.1_51485_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc094d05-ba43-4f0f-bd16-9948d5004a2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445255.1_51485_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:26,047] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:26,052] [INFO] Selected 24 target genomes.
[2024-01-24 10:58:26,052] [INFO] Target genome list was writen to GCF_900445255.1_51485_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:26,133] [INFO] Task started: fastANI
[2024-01-24 10:58:26,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b80697-02c1-4f9b-9baf-3f34ee312d45/GCF_900445255.1_51485_H01_genomic.fna.gz --refList GCF_900445255.1_51485_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445255.1_51485_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:37,006] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:37,022] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:37,022] [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_900445255.1	s__Anaerobiospirillum_A thomasii	100.0	979	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Anaerobiospirillum_A	95.0	98.91	98.91	0.82	0.82	2	conclusive
GCA_905186145.1	s__Succinivibrio sp905186145	78.4947	76	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203285.1	s__Succinatimonas sp905203285	77.4263	59	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188195.1	s__Succinatimonas hippei	77.2462	57	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinatimonas	95.0	98.70	97.40	0.92	0.85	3	-
GCF_900167015.1	s__Succinivibrio dextrinosolvens	77.2199	62	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	96.59	96.11	0.85	0.83	6	-
GCA_900316175.1	s__Succinivibrio sp900316175	76.6486	81	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	99.29	98.66	0.86	0.80	9	-
GCA_900317105.1	s__Succinivibrio sp900317105	76.5554	62	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	98.54	96.63	0.90	0.79	4	-
GCF_900116345.1	s__Succinivibrio dextrinosolvens_B	76.5022	75	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000431835.1	s__Succinivibrio sp000431835	76.4213	70	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	97.12	95.78	0.87	0.82	11	-
GCA_905201175.1	s__Succinivibrio sp905201175	76.2111	54	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Succinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694225.1	s__Avisuccinivibrio stercorigallinarum	76.1266	80	996	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Succinivibrionaceae;g__Avisuccinivibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,025] [INFO] GTDB search result was written to GCF_900445255.1_51485_H01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:37,026] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:37,029] [INFO] DFAST_QC result json was written to GCF_900445255.1_51485_H01_genomic.fna/dqc_result.json
[2024-01-24 10:58:37,029] [INFO] DFAST_QC completed!
[2024-01-24 10:58:37,029] [INFO] Total running time: 0h0m59s