[2023-06-13 17:55:50,376] [INFO] DFAST_QC pipeline started.
[2023-06-13 17:55:50,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 17:55:50,378] [INFO] DQC Reference Directory: /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference
[2023-06-13 17:55:51,620] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 17:55:51,621] [INFO] Task started: Prodigal
[2023-06-13 17:55:51,621] [INFO] Running command: gunzip -c /var/lib/cwl/stg969c658f-d620-4b44-aec7-a643f6dc9c95/GCA_022793175.1_ASM2279317v1_genomic.fna.gz | prodigal -d GCA_022793175.1_ASM2279317v1_genomic.fna/cds.fna -a GCA_022793175.1_ASM2279317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 17:56:00,033] [INFO] Task succeeded: Prodigal
[2023-06-13 17:56:00,033] [INFO] Task started: HMMsearch
[2023-06-13 17:56:00,033] [INFO] Running command: hmmsearch --tblout GCA_022793175.1_ASM2279317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/reference_markers.hmm GCA_022793175.1_ASM2279317v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 17:56:00,287] [INFO] Task succeeded: HMMsearch
[2023-06-13 17:56:00,289] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg969c658f-d620-4b44-aec7-a643f6dc9c95/GCA_022793175.1_ASM2279317v1_genomic.fna.gz]
[2023-06-13 17:56:00,327] [INFO] Query marker FASTA was written to GCA_022793175.1_ASM2279317v1_genomic.fna/markers.fasta
[2023-06-13 17:56:00,327] [INFO] Task started: Blastn
[2023-06-13 17:56:00,327] [INFO] Running command: blastn -query GCA_022793175.1_ASM2279317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/reference_markers.fasta -out GCA_022793175.1_ASM2279317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:00,895] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:00,901] [INFO] Selected 21 target genomes.
[2023-06-13 17:56:00,901] [INFO] Target genome list was writen to GCA_022793175.1_ASM2279317v1_genomic.fna/target_genomes.txt
[2023-06-13 17:56:00,902] [INFO] Task started: fastANI
[2023-06-13 17:56:00,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg969c658f-d620-4b44-aec7-a643f6dc9c95/GCA_022793175.1_ASM2279317v1_genomic.fna.gz --refList GCA_022793175.1_ASM2279317v1_genomic.fna/target_genomes.txt --output GCA_022793175.1_ASM2279317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 17:56:14,362] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:14,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 17:56:14,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 17:56:14,373] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 17:56:14,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 17:56:14,374] [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
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.4392	288	1028	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	76.0244	64	1028	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	75.9341	70	1028	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	75.8869	50	1028	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 17:56:14,376] [INFO] DFAST Taxonomy check result was written to GCA_022793175.1_ASM2279317v1_genomic.fna/tc_result.tsv
[2023-06-13 17:56:14,377] [INFO] ===== Taxonomy check completed =====
[2023-06-13 17:56:14,378] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 17:56:14,378] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/checkm_data
[2023-06-13 17:56:14,379] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 17:56:14,416] [INFO] Task started: CheckM
[2023-06-13 17:56:14,416] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022793175.1_ASM2279317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022793175.1_ASM2279317v1_genomic.fna/checkm_input GCA_022793175.1_ASM2279317v1_genomic.fna/checkm_result
[2023-06-13 17:56:44,257] [INFO] Task succeeded: CheckM
[2023-06-13 17:56:44,258] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 17:56:44,285] [INFO] ===== Completeness check finished =====
[2023-06-13 17:56:44,285] [INFO] ===== Start GTDB Search =====
[2023-06-13 17:56:44,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022793175.1_ASM2279317v1_genomic.fna/markers.fasta)
[2023-06-13 17:56:44,286] [INFO] Task started: Blastn
[2023-06-13 17:56:44,286] [INFO] Running command: blastn -query GCA_022793175.1_ASM2279317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg022329c2-9d75-4ca8-b5ef-9b7a3e977163/dqc_reference/reference_markers_gtdb.fasta -out GCA_022793175.1_ASM2279317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 17:56:45,068] [INFO] Task succeeded: Blastn
[2023-06-13 17:56:45,073] [INFO] Selected 7 target genomes.
[2023-06-13 17:56:45,073] [INFO] Target genome list was writen to GCA_022793175.1_ASM2279317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 17:56:45,075] [INFO] Task started: fastANI
[2023-06-13 17:56:45,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg969c658f-d620-4b44-aec7-a643f6dc9c95/GCA_022793175.1_ASM2279317v1_genomic.fna.gz --refList GCA_022793175.1_ASM2279317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022793175.1_ASM2279317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 17:56:51,900] [INFO] Task succeeded: fastANI
[2023-06-13 17:56:51,911] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 17:56:51,911] [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_910576125.1	s__Acetatifactor sp910576125	99.4234	992	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_910585425.1	s__Acetatifactor sp910585425	82.505	707	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585615.1	s__Acetatifactor sp910585615	82.3269	643	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585665.1	s__Acetatifactor sp910585665	81.5763	576	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584235.1	s__Acetatifactor sp910584235	81.4141	582	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612485.1	s__Acetatifactor sp003612485	77.9346	298	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.96	98.96	0.94	0.94	2	-
GCA_910586215.1	s__Acetatifactor sp910586215	76.825	225	1028	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 17:56:51,914] [INFO] GTDB search result was written to GCA_022793175.1_ASM2279317v1_genomic.fna/result_gtdb.tsv
[2023-06-13 17:56:51,914] [INFO] ===== GTDB Search completed =====
[2023-06-13 17:56:51,917] [INFO] DFAST_QC result json was written to GCA_022793175.1_ASM2279317v1_genomic.fna/dqc_result.json
[2023-06-13 17:56:51,918] [INFO] DFAST_QC completed!
[2023-06-13 17:56:51,918] [INFO] Total running time: 0h1m2s