[2024-01-24 14:23:17,897] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:17,899] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:17,899] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference
[2024-01-24 14:23:19,149] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:19,150] [INFO] Task started: Prodigal
[2024-01-24 14:23:19,151] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dfe9e79-2776-4172-977d-5f59647e1430/GCF_019448085.1_ASM1944808v1_genomic.fna.gz | prodigal -d GCF_019448085.1_ASM1944808v1_genomic.fna/cds.fna -a GCF_019448085.1_ASM1944808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:27,190] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:27,191] [INFO] Task started: HMMsearch
[2024-01-24 14:23:27,191] [INFO] Running command: hmmsearch --tblout GCF_019448085.1_ASM1944808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/reference_markers.hmm GCF_019448085.1_ASM1944808v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:27,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:27,538] [INFO] Found 6/6 markers.
[2024-01-24 14:23:27,586] [INFO] Query marker FASTA was written to GCF_019448085.1_ASM1944808v1_genomic.fna/markers.fasta
[2024-01-24 14:23:27,588] [INFO] Task started: Blastn
[2024-01-24 14:23:27,588] [INFO] Running command: blastn -query GCF_019448085.1_ASM1944808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/reference_markers.fasta -out GCF_019448085.1_ASM1944808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:28,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:28,344] [INFO] Selected 13 target genomes.
[2024-01-24 14:23:28,345] [INFO] Target genome list was writen to GCF_019448085.1_ASM1944808v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:28,354] [INFO] Task started: fastANI
[2024-01-24 14:23:28,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dfe9e79-2776-4172-977d-5f59647e1430/GCF_019448085.1_ASM1944808v1_genomic.fna.gz --refList GCF_019448085.1_ASM1944808v1_genomic.fna/target_genomes.txt --output GCF_019448085.1_ASM1944808v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:34,223] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:34,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:34,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:34,232] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:23:34,232] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:23:34,232] [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
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	78.6535	289	998	95	below_threshold
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	78.0099	133	998	95	below_threshold
Clostridium merdae	strain=Marseille-P2953	GCA_900176635.1	1958780	1958780	type	True	77.141	56	998	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.1361	130	998	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.7734	110	998	95	below_threshold
Caproicibacterium amylolyticum	strain=LBM18003	GCA_014467055.1	2766537	2766537	type	True	76.5172	66	998	95	below_threshold
Yeguia hominis	strain=NSJ-40	GCA_014384705.1	2763662	2763662	type	True	76.3823	52	998	95	below_threshold
Caproicibacterium lactatifermentans	strain=LBM19010	GCA_013315815.1	2666138	2666138	type	True	76.2966	50	998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:34,234] [INFO] DFAST Taxonomy check result was written to GCF_019448085.1_ASM1944808v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:34,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:34,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:34,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/checkm_data
[2024-01-24 14:23:34,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:34,267] [INFO] Task started: CheckM
[2024-01-24 14:23:34,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019448085.1_ASM1944808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019448085.1_ASM1944808v1_genomic.fna/checkm_input GCF_019448085.1_ASM1944808v1_genomic.fna/checkm_result
[2024-01-24 14:24:05,723] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:05,724] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,743] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:05,744] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:05,744] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019448085.1_ASM1944808v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:05,745] [INFO] Task started: Blastn
[2024-01-24 14:24:05,745] [INFO] Running command: blastn -query GCF_019448085.1_ASM1944808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1028595-176a-4867-8a35-f95a1eeebec2/dqc_reference/reference_markers_gtdb.fasta -out GCF_019448085.1_ASM1944808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:06,894] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:06,897] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:06,897] [INFO] Target genome list was writen to GCF_019448085.1_ASM1944808v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:06,909] [INFO] Task started: fastANI
[2024-01-24 14:24:06,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dfe9e79-2776-4172-977d-5f59647e1430/GCF_019448085.1_ASM1944808v1_genomic.fna.gz --refList GCF_019448085.1_ASM1944808v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019448085.1_ASM1944808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:12,568] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:12,589] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:24:12,590] [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_000752215.1	s__Caproiciproducens sp000752215	85.1043	715	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	98.70	97.09	0.94	0.88	5	-
GCA_900546895.1	s__Caproiciproducens sp900546895	84.3675	508	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_002359465.1	s__Caproiciproducens sp002359465	82.8506	535	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_012516295.1	s__Caproiciproducens sp012516295	78.9542	180	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	-
GCF_004768785.1	s__Caproiciproducens galactitolivorans	78.6581	289	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproiciproducens	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002338255.1	s__Caproiciproducens sp002338255	78.4584	260	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_002378845.1	s__Caproiciproducens sp002378845	78.3091	247	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_012517675.1	s__Caproiciproducens sp012517675	77.8852	190	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	-
GCF_900176635.1	s__Clostridium_E merdae	77.141	56	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900550095.1	s__UMGS1264 sp900550095	76.8038	50	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1264	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:12,594] [INFO] GTDB search result was written to GCF_019448085.1_ASM1944808v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:12,595] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:12,599] [INFO] DFAST_QC result json was written to GCF_019448085.1_ASM1944808v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:12,599] [INFO] DFAST_QC completed!
[2024-01-24 14:24:12,599] [INFO] Total running time: 0h0m55s