[2024-01-24 13:52:12,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:52:12,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:52:12,009] [INFO] DQC Reference Directory: /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference
[2024-01-24 13:52:13,266] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:52:13,267] [INFO] Task started: Prodigal
[2024-01-24 13:52:13,267] [INFO] Running command: gunzip -c /var/lib/cwl/stg593f1d1c-4028-4424-9614-ab88938e83ef/GCF_014647355.1_ASM1464735v1_genomic.fna.gz | prodigal -d GCF_014647355.1_ASM1464735v1_genomic.fna/cds.fna -a GCF_014647355.1_ASM1464735v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:52:41,771] [INFO] Task succeeded: Prodigal
[2024-01-24 13:52:41,772] [INFO] Task started: HMMsearch
[2024-01-24 13:52:41,772] [INFO] Running command: hmmsearch --tblout GCF_014647355.1_ASM1464735v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/reference_markers.hmm GCF_014647355.1_ASM1464735v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:52:42,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:52:42,088] [INFO] Found 6/6 markers.
[2024-01-24 13:52:42,134] [INFO] Query marker FASTA was written to GCF_014647355.1_ASM1464735v1_genomic.fna/markers.fasta
[2024-01-24 13:52:42,135] [INFO] Task started: Blastn
[2024-01-24 13:52:42,135] [INFO] Running command: blastn -query GCF_014647355.1_ASM1464735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/reference_markers.fasta -out GCF_014647355.1_ASM1464735v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:42,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:42,706] [INFO] Selected 9 target genomes.
[2024-01-24 13:52:42,706] [INFO] Target genome list was writen to GCF_014647355.1_ASM1464735v1_genomic.fna/target_genomes.txt
[2024-01-24 13:52:42,711] [INFO] Task started: fastANI
[2024-01-24 13:52:42,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg593f1d1c-4028-4424-9614-ab88938e83ef/GCF_014647355.1_ASM1464735v1_genomic.fna.gz --refList GCF_014647355.1_ASM1464735v1_genomic.fna/target_genomes.txt --output GCF_014647355.1_ASM1464735v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:52:52,866] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:52,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:52:52,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:52:52,878] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:52:52,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:52:52,878] [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
Butyricimonas paravirosa	strain=JCM 18677	GCA_014647355.1	1472417	1472417	type	True	100.0	1824	1826	95	conclusive
Butyricimonas paravirosa	strain=DSM 105722	GCA_011927845.1	1472417	1472417	type	True	99.9991	1821	1826	95	conclusive
Butyricimonas faecihominis	strain=JCM 18676	GCA_014647335.1	1472416	1472416	type	True	94.8615	1186	1826	95	below_threshold
Butyricimonas faecihominis	strain=DSM 105721	GCA_014196975.1	1472416	1472416	type	True	94.8367	1201	1826	95	below_threshold
Butyricimonas faecihominis	strain=CCUG 65562	GCA_008830385.1	1472416	1472416	type	True	94.7829	1193	1826	95	below_threshold
Butyricimonas virosa	strain=DSM 23226	GCA_025148635.1	544645	544645	type	True	91.7506	1133	1826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:52:52,880] [INFO] DFAST Taxonomy check result was written to GCF_014647355.1_ASM1464735v1_genomic.fna/tc_result.tsv
[2024-01-24 13:52:52,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:52:52,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:52:52,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/checkm_data
[2024-01-24 13:52:52,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:52:52,936] [INFO] Task started: CheckM
[2024-01-24 13:52:52,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647355.1_ASM1464735v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647355.1_ASM1464735v1_genomic.fna/checkm_input GCF_014647355.1_ASM1464735v1_genomic.fna/checkm_result
[2024-01-24 13:54:10,240] [INFO] Task succeeded: CheckM
[2024-01-24 13:54:10,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:54:10,262] [INFO] ===== Completeness check finished =====
[2024-01-24 13:54:10,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:54:10,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647355.1_ASM1464735v1_genomic.fna/markers.fasta)
[2024-01-24 13:54:10,264] [INFO] Task started: Blastn
[2024-01-24 13:54:10,264] [INFO] Running command: blastn -query GCF_014647355.1_ASM1464735v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb61064cf-e879-4528-bed7-a00f7a34f212/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647355.1_ASM1464735v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:11,075] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:11,079] [INFO] Selected 7 target genomes.
[2024-01-24 13:54:11,080] [INFO] Target genome list was writen to GCF_014647355.1_ASM1464735v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:54:11,109] [INFO] Task started: fastANI
[2024-01-24 13:54:11,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg593f1d1c-4028-4424-9614-ab88938e83ef/GCF_014647355.1_ASM1464735v1_genomic.fna.gz --refList GCF_014647355.1_ASM1464735v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647355.1_ASM1464735v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:54:19,547] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:19,554] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:54:19,554] [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_011927845.1	s__Butyricimonas paravirosa	99.9991	1821	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.86	97.78	0.90	0.83	11	conclusive
GCF_014647335.1	s__Butyricimonas faecihominis	94.8731	1185	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.47	98.30	0.95	0.86	7	-
GCF_000519105.1	s__Butyricimonas virosa	91.8555	1118	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.30	95.30	0.86	0.78	18	-
GCF_003991565.1	s__Butyricimonas faecalis	87.6334	1009	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	98.78	97.96	0.89	0.85	6	-
GCA_019117165.1	s__Butyricimonas faecavium	87.4124	789	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761485.1	s__Butyricimonas sp900761485	83.9549	835	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003479425.1	s__Butyricimonas sp003479425	81.5076	938	1826	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Butyricimonas	95.0	99.97	99.94	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:54:19,556] [INFO] GTDB search result was written to GCF_014647355.1_ASM1464735v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:54:19,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:54:19,559] [INFO] DFAST_QC result json was written to GCF_014647355.1_ASM1464735v1_genomic.fna/dqc_result.json
[2024-01-24 13:54:19,559] [INFO] DFAST_QC completed!
[2024-01-24 13:54:19,559] [INFO] Total running time: 0h2m8s