[2024-01-25 17:53:50,717] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference
[2024-01-25 17:53:51,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,907] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bb581ea-7cbe-4c49-a0f3-86b64164064d/GCF_014467055.1_ASM1446705v1_genomic.fna.gz | prodigal -d GCF_014467055.1_ASM1446705v1_genomic.fna/cds.fna -a GCF_014467055.1_ASM1446705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:59,592] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:59,593] [INFO] Task started: HMMsearch
[2024-01-25 17:53:59,593] [INFO] Running command: hmmsearch --tblout GCF_014467055.1_ASM1446705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/reference_markers.hmm GCF_014467055.1_ASM1446705v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:59,802] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:59,803] [INFO] Found 6/6 markers.
[2024-01-25 17:53:59,828] [INFO] Query marker FASTA was written to GCF_014467055.1_ASM1446705v1_genomic.fna/markers.fasta
[2024-01-25 17:53:59,828] [INFO] Task started: Blastn
[2024-01-25 17:53:59,828] [INFO] Running command: blastn -query GCF_014467055.1_ASM1446705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/reference_markers.fasta -out GCF_014467055.1_ASM1446705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:00,368] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:00,370] [INFO] Selected 17 target genomes.
[2024-01-25 17:54:00,370] [INFO] Target genome list was writen to GCF_014467055.1_ASM1446705v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:00,376] [INFO] Task started: fastANI
[2024-01-25 17:54:00,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb581ea-7cbe-4c49-a0f3-86b64164064d/GCF_014467055.1_ASM1446705v1_genomic.fna.gz --refList GCF_014467055.1_ASM1446705v1_genomic.fna/target_genomes.txt --output GCF_014467055.1_ASM1446705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:08,848] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:08,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:08,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:08,855] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:08,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:08,855] [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
Caproicibacterium amylolyticum	strain=LBM18003	GCA_014467055.1	2766537	2766537	type	True	100.0	997	998	95	conclusive
Caproicibacterium lactatifermentans	strain=LBM19010	GCA_013315815.1	2666138	2666138	type	True	79.9919	253	998	95	below_threshold
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	76.6348	53	998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:08,856] [INFO] DFAST Taxonomy check result was written to GCF_014467055.1_ASM1446705v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:08,857] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:08,857] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:08,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/checkm_data
[2024-01-25 17:54:08,858] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:08,890] [INFO] Task started: CheckM
[2024-01-25 17:54:08,890] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014467055.1_ASM1446705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014467055.1_ASM1446705v1_genomic.fna/checkm_input GCF_014467055.1_ASM1446705v1_genomic.fna/checkm_result
[2024-01-25 17:54:35,105] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:35,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:35,132] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:35,132] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:35,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014467055.1_ASM1446705v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:35,132] [INFO] Task started: Blastn
[2024-01-25 17:54:35,133] [INFO] Running command: blastn -query GCF_014467055.1_ASM1446705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c482eb8-a595-482a-9123-df7983f5dc9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014467055.1_ASM1446705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:35,989] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:35,991] [INFO] Selected 21 target genomes.
[2024-01-25 17:54:35,992] [INFO] Target genome list was writen to GCF_014467055.1_ASM1446705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:36,013] [INFO] Task started: fastANI
[2024-01-25 17:54:36,013] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bb581ea-7cbe-4c49-a0f3-86b64164064d/GCF_014467055.1_ASM1446705v1_genomic.fna.gz --refList GCF_014467055.1_ASM1446705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014467055.1_ASM1446705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:44,331] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:44,337] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:54:44,337] [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_014467055.1	s__Caproicibacterium amylolyticum	100.0	997	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	98.85	98.85	0.89	0.89	2	conclusive
GCA_002119605.1	s__Caproicibacterium sp002119605	79.9665	251	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.88	99.69	0.99	0.94	26	-
GCA_902809935.1	s__Caproicibacterium sp902809935	78.4795	62	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338255.1	s__Caproiciproducens sp002338255	77.693	51	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399445.1	s__Caproicibacterium sp002399445	77.6009	211	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.23	98.41	0.93	0.89	8	-
GCA_900554535.1	s__Caproicibacterium sp900554535	77.4259	64	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacterium	95.0	99.83	99.83	0.87	0.87	2	-
GCA_012517675.1	s__Caproiciproducens sp012517675	76.6412	55	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715025.1	s__Caccousia avistercoris	75.8815	53	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.39	98.39	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:44,339] [INFO] GTDB search result was written to GCF_014467055.1_ASM1446705v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:44,340] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:44,342] [INFO] DFAST_QC result json was written to GCF_014467055.1_ASM1446705v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:44,342] [INFO] DFAST_QC completed!
[2024-01-25 17:54:44,342] [INFO] Total running time: 0h0m54s