[2024-01-25 18:53:21,043] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:21,045] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:21,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference
[2024-01-25 18:53:22,140] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:22,144] [INFO] Task started: Prodigal
[2024-01-25 18:53:22,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg6953b9ce-af18-4332-ba32-86c676e78b7f/GCF_000024665.1_ASM2466v1_genomic.fna.gz | prodigal -d GCF_000024665.1_ASM2466v1_genomic.fna/cds.fna -a GCF_000024665.1_ASM2466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:31,887] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:31,887] [INFO] Task started: HMMsearch
[2024-01-25 18:53:31,887] [INFO] Running command: hmmsearch --tblout GCF_000024665.1_ASM2466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/reference_markers.hmm GCF_000024665.1_ASM2466v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:32,115] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:32,116] [INFO] Found 6/6 markers.
[2024-01-25 18:53:32,145] [INFO] Query marker FASTA was written to GCF_000024665.1_ASM2466v1_genomic.fna/markers.fasta
[2024-01-25 18:53:32,146] [INFO] Task started: Blastn
[2024-01-25 18:53:32,146] [INFO] Running command: blastn -query GCF_000024665.1_ASM2466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/reference_markers.fasta -out GCF_000024665.1_ASM2466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:32,684] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:32,687] [INFO] Selected 13 target genomes.
[2024-01-25 18:53:32,687] [INFO] Target genome list was writen to GCF_000024665.1_ASM2466v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:32,696] [INFO] Task started: fastANI
[2024-01-25 18:53:32,697] [INFO] Running command: fastANI --query /var/lib/cwl/stg6953b9ce-af18-4332-ba32-86c676e78b7f/GCF_000024665.1_ASM2466v1_genomic.fna.gz --refList GCF_000024665.1_ASM2466v1_genomic.fna/target_genomes.txt --output GCF_000024665.1_ASM2466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:42,907] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:42,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:42,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:42,912] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:53:42,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:42,913] [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
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	100.0	1279	1280	95	conclusive
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	99.9915	1278	1280	95	conclusive
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	79.6323	227	1280	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	78.1794	104	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:42,914] [INFO] DFAST Taxonomy check result was written to GCF_000024665.1_ASM2466v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:42,915] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:42,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:42,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/checkm_data
[2024-01-25 18:53:42,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:42,954] [INFO] Task started: CheckM
[2024-01-25 18:53:42,954] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024665.1_ASM2466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024665.1_ASM2466v1_genomic.fna/checkm_input GCF_000024665.1_ASM2466v1_genomic.fna/checkm_result
[2024-01-25 18:54:14,214] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:14,215] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.85%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:14,236] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:14,236] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:14,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024665.1_ASM2466v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:14,237] [INFO] Task started: Blastn
[2024-01-25 18:54:14,237] [INFO] Running command: blastn -query GCF_000024665.1_ASM2466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6ac0c76-ecfd-4c8a-8697-1f258598496d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024665.1_ASM2466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:15,026] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:15,029] [INFO] Selected 8 target genomes.
[2024-01-25 18:54:15,029] [INFO] Target genome list was writen to GCF_000024665.1_ASM2466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:15,043] [INFO] Task started: fastANI
[2024-01-25 18:54:15,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg6953b9ce-af18-4332-ba32-86c676e78b7f/GCF_000024665.1_ASM2466v1_genomic.fna.gz --refList GCF_000024665.1_ASM2466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024665.1_ASM2466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:23,205] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:23,211] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:23,211] [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_000146505.1	s__Fibrobacter succinogenes	99.9915	1278	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002210425.1	s__Fibrobacter elongatus	93.3473	993	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.37	97.19	0.91	0.89	4	-
GCF_900177805.1	s__Fibrobacter sp900177805	92.085	984	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.22	97.22	0.89	0.89	2	-
GCF_900215325.1	s__Fibrobacter sp900215325	91.5251	943	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.50	97.09	0.94	0.94	6	-
GCA_902791475.1	s__Fibrobacter succinogenes_J	91.1774	914	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.39	95.39	0.76	0.76	2	-
GCA_002394865.1	s__Fibrobacter sp002394865	90.6697	964	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002210345.1	s__Fibrobacter sp002210345	89.211	899	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.16	96.29	0.89	0.80	6	-
GCA_902779965.1	s__Fibrobacter succinogenes_F	85.8978	875	1280	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:23,212] [INFO] GTDB search result was written to GCF_000024665.1_ASM2466v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:23,213] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:23,215] [INFO] DFAST_QC result json was written to GCF_000024665.1_ASM2466v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:23,215] [INFO] DFAST_QC completed!
[2024-01-25 18:54:23,215] [INFO] Total running time: 0h1m2s