[2024-01-24 14:55:07,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:07,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:07,988] [INFO] DQC Reference Directory: /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference
[2024-01-24 14:55:09,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:09,681] [INFO] Task started: Prodigal
[2024-01-24 14:55:09,681] [INFO] Running command: gunzip -c /var/lib/cwl/stga19151c7-1e89-4ce5-8d38-9d6c62783421/GCF_009746625.1_ASM974662v1_genomic.fna.gz | prodigal -d GCF_009746625.1_ASM974662v1_genomic.fna/cds.fna -a GCF_009746625.1_ASM974662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:19,310] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:19,310] [INFO] Task started: HMMsearch
[2024-01-24 14:55:19,311] [INFO] Running command: hmmsearch --tblout GCF_009746625.1_ASM974662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/reference_markers.hmm GCF_009746625.1_ASM974662v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:19,607] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:19,609] [INFO] Found 6/6 markers.
[2024-01-24 14:55:19,652] [INFO] Query marker FASTA was written to GCF_009746625.1_ASM974662v1_genomic.fna/markers.fasta
[2024-01-24 14:55:19,652] [INFO] Task started: Blastn
[2024-01-24 14:55:19,652] [INFO] Running command: blastn -query GCF_009746625.1_ASM974662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/reference_markers.fasta -out GCF_009746625.1_ASM974662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:20,291] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:20,295] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:20,296] [INFO] Target genome list was writen to GCF_009746625.1_ASM974662v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:20,306] [INFO] Task started: fastANI
[2024-01-24 14:55:20,307] [INFO] Running command: fastANI --query /var/lib/cwl/stga19151c7-1e89-4ce5-8d38-9d6c62783421/GCF_009746625.1_ASM974662v1_genomic.fna.gz --refList GCF_009746625.1_ASM974662v1_genomic.fna/target_genomes.txt --output GCF_009746625.1_ASM974662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:28,323] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:28,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:28,325] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:28,333] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:28,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:28,333] [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
Caproicibacter fermentans	strain=EA1	GCA_009746625.1	2576756	2576756	type	True	100.0	1240	1244	95	conclusive
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	77.3942	95	1244	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	77.2896	105	1244	95	below_threshold
Caproiciproducens galactitolivorans	strain=BS-1	GCA_004768785.1	642589	642589	type	True	76.9634	98	1244	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	76.7313	62	1244	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:28,335] [INFO] DFAST Taxonomy check result was written to GCF_009746625.1_ASM974662v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:28,336] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:28,336] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:28,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/checkm_data
[2024-01-24 14:55:28,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:28,378] [INFO] Task started: CheckM
[2024-01-24 14:55:28,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009746625.1_ASM974662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009746625.1_ASM974662v1_genomic.fna/checkm_input GCF_009746625.1_ASM974662v1_genomic.fna/checkm_result
[2024-01-24 14:56:01,828] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:01,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:01,856] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:01,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:01,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009746625.1_ASM974662v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:01,857] [INFO] Task started: Blastn
[2024-01-24 14:56:01,858] [INFO] Running command: blastn -query GCF_009746625.1_ASM974662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga08bcd27-bf91-43fa-9a0f-b923b762c7cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_009746625.1_ASM974662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:02,778] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:02,782] [INFO] Selected 20 target genomes.
[2024-01-24 14:56:02,782] [INFO] Target genome list was writen to GCF_009746625.1_ASM974662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:02,828] [INFO] Task started: fastANI
[2024-01-24 14:56:02,829] [INFO] Running command: fastANI --query /var/lib/cwl/stga19151c7-1e89-4ce5-8d38-9d6c62783421/GCF_009746625.1_ASM974662v1_genomic.fna.gz --refList GCF_009746625.1_ASM974662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009746625.1_ASM974662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:12,670] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:12,682] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:12,682] [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_009746625.1	s__Caproicibacter fermentans	100.0	1240	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	98.75	98.55	0.84	0.84	3	conclusive
GCF_004103755.1	s__Caproicibacter sp004103755	80.9412	473	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900184925.1	s__Caproicibacter sp900184925	79.2112	165	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752215.1	s__Caproiciproducens sp000752215	78.3618	177	1244	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_002399225.1	s__Caproicibacter sp002399225	78.215	201	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caproicibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810075.1	s__Clostridium_E sp002397665	78.1223	134	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Clostridium_E	95.0	97.21	97.21	0.87	0.87	2	-
GCA_012517675.1	s__Caproiciproducens sp012517675	77.7809	125	1244	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_900546895.1	s__Caproiciproducens sp900546895	77.5476	129	1244	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_001261775.1	s__Anaeromassilibacillus senegalensis	77.3442	103	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002359465.1	s__Caproiciproducens sp002359465	77.2917	114	1244	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_002159845.1	s__Anaeromassilibacillus stercoravium	76.8922	81	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	98.79	98.27	0.94	0.87	13	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	76.8586	93	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712435.1	s__Caccousia avicola	76.4419	76	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.29	98.29	0.88	0.88	2	-
GCA_018715025.1	s__Caccousia avistercoris	75.9608	67	1244	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.39	98.39	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:12,684] [INFO] GTDB search result was written to GCF_009746625.1_ASM974662v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:12,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:12,688] [INFO] DFAST_QC result json was written to GCF_009746625.1_ASM974662v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:12,688] [INFO] DFAST_QC completed!
[2024-01-24 14:56:12,688] [INFO] Total running time: 0h1m5s