[2024-01-24 13:41:18,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:18,930] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:18,930] [INFO] DQC Reference Directory: /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference
[2024-01-24 13:41:20,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,269] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,269] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4b52a5f-23c8-4938-9927-155bacee430c/GCF_009696445.1_ASM969644v1_genomic.fna.gz | prodigal -d GCF_009696445.1_ASM969644v1_genomic.fna/cds.fna -a GCF_009696445.1_ASM969644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:28,806] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:28,806] [INFO] Task started: HMMsearch
[2024-01-24 13:41:28,806] [INFO] Running command: hmmsearch --tblout GCF_009696445.1_ASM969644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/reference_markers.hmm GCF_009696445.1_ASM969644v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:29,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:29,179] [INFO] Found 6/6 markers.
[2024-01-24 13:41:29,210] [INFO] Query marker FASTA was written to GCF_009696445.1_ASM969644v1_genomic.fna/markers.fasta
[2024-01-24 13:41:29,211] [INFO] Task started: Blastn
[2024-01-24 13:41:29,211] [INFO] Running command: blastn -query GCF_009696445.1_ASM969644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/reference_markers.fasta -out GCF_009696445.1_ASM969644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,941] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,944] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:29,945] [INFO] Target genome list was writen to GCF_009696445.1_ASM969644v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,953] [INFO] Task started: fastANI
[2024-01-24 13:41:29,953] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4b52a5f-23c8-4938-9927-155bacee430c/GCF_009696445.1_ASM969644v1_genomic.fna.gz --refList GCF_009696445.1_ASM969644v1_genomic.fna/target_genomes.txt --output GCF_009696445.1_ASM969644v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:45,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,727] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:45,728] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:45,733] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:45,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:45,733] [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
Porcincola intestinalis	strain=Oil+RF-744-WCA-WT-11	GCA_009696445.1	2606632	2606632	type	True	100.0	1028	1031	95	conclusive
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	79.1027	59	1031	95	below_threshold
Bilifractor porci	strain=Oil+RF-744-WCA-WT-13	GCA_009696005.1	2606636	2606636	type	True	77.6324	50	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:45,735] [INFO] DFAST Taxonomy check result was written to GCF_009696445.1_ASM969644v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:45,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:45,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:45,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/checkm_data
[2024-01-24 13:41:45,737] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:45,770] [INFO] Task started: CheckM
[2024-01-24 13:41:45,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696445.1_ASM969644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696445.1_ASM969644v1_genomic.fna/checkm_input GCF_009696445.1_ASM969644v1_genomic.fna/checkm_result
[2024-01-24 13:42:17,523] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:17,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:17,548] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:17,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:17,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696445.1_ASM969644v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:17,550] [INFO] Task started: Blastn
[2024-01-24 13:42:17,550] [INFO] Running command: blastn -query GCF_009696445.1_ASM969644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg576b469b-27a5-443a-8002-c29a1959610a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696445.1_ASM969644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:18,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:18,634] [INFO] Selected 15 target genomes.
[2024-01-24 13:42:18,634] [INFO] Target genome list was writen to GCF_009696445.1_ASM969644v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:18,681] [INFO] Task started: fastANI
[2024-01-24 13:42:18,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4b52a5f-23c8-4938-9927-155bacee430c/GCF_009696445.1_ASM969644v1_genomic.fna.gz --refList GCF_009696445.1_ASM969644v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696445.1_ASM969644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:26,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:26,045] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:26,046] [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_009696445.1	s__Porcincola intestinalis	100.0	1028	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	97.03	96.19	0.86	0.71	6	conclusive
GCA_902761585.1	s__Porcincola sp902800805	94.8509	671	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.06	97.58	0.81	0.65	18	-
GCA_900555005.1	s__Porcincola sp900555005	91.0824	437	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	99.94	99.94	0.95	0.95	2	-
GCA_002482005.1	s__Porcincola sp002482005	78.8892	274	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799015.1	s__Porcincola sp902799015	78.2723	95	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.95	98.88	0.78	0.76	3	-
GCA_902781455.1	s__Porcincola sp902781455	77.4407	94	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797665.1	s__Porcincola sp902797665	77.2899	87	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235415.1	s__Porcincola sp905235415	76.9237	100	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002392705.1	s__Porcincola sp002392705	76.8686	91	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779575.1	s__Porcincola sp902779575	76.7679	117	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.91	98.90	0.94	0.92	3	-
GCA_902803155.1	s__Porcincola sp902803155	75.676	62	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767065.1	s__Porcincola sp902767065	75.6165	53	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Porcincola	95.0	98.57	98.57	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:26,048] [INFO] GTDB search result was written to GCF_009696445.1_ASM969644v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:26,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:26,053] [INFO] DFAST_QC result json was written to GCF_009696445.1_ASM969644v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:26,053] [INFO] DFAST_QC completed!
[2024-01-24 13:42:26,054] [INFO] Total running time: 0h1m7s