[2023-06-05 09:36:50,644] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:36:50,646] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:36:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference
[2023-06-05 09:36:52,334] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:36:52,335] [INFO] Task started: Prodigal
[2023-06-05 09:36:52,336] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f5ef0c4-ab63-404b-ae86-e04e3b59d899/GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna.gz | prodigal -d GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/cds.fna -a GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:37:01,028] [INFO] Task succeeded: Prodigal
[2023-06-05 09:37:01,029] [INFO] Task started: HMMsearch
[2023-06-05 09:37:01,029] [INFO] Running command: hmmsearch --tblout GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/reference_markers.hmm GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:37:01,343] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:37:01,345] [INFO] Found 6/6 markers.
[2023-06-05 09:37:01,375] [INFO] Query marker FASTA was written to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/markers.fasta
[2023-06-05 09:37:01,376] [INFO] Task started: Blastn
[2023-06-05 09:37:01,376] [INFO] Running command: blastn -query GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/reference_markers.fasta -out GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:02,040] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:02,050] [INFO] Selected 15 target genomes.
[2023-06-05 09:37:02,051] [INFO] Target genome list was writen to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/target_genomes.txt
[2023-06-05 09:37:02,057] [INFO] Task started: fastANI
[2023-06-05 09:37:02,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5ef0c4-ab63-404b-ae86-e04e3b59d899/GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna.gz --refList GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/target_genomes.txt --output GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:37:12,935] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:12,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:37:12,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:37:12,942] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:37:12,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:37:12,942] [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_000146505.1	834	833	type	True	91.4518	759	912	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	91.3714	758	912	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.6185	140	912	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	77.9202	69	912	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:37:12,959] [INFO] DFAST Taxonomy check result was written to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/tc_result.tsv
[2023-06-05 09:37:12,960] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:37:12,960] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:37:12,960] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/checkm_data
[2023-06-05 09:37:12,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:37:13,008] [INFO] Task started: CheckM
[2023-06-05 09:37:13,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/checkm_input GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/checkm_result
[2023-06-05 09:37:42,906] [INFO] Task succeeded: CheckM
[2023-06-05 09:37:42,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:37:42,932] [INFO] ===== Completeness check finished =====
[2023-06-05 09:37:42,933] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:37:42,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/markers.fasta)
[2023-06-05 09:37:42,934] [INFO] Task started: Blastn
[2023-06-05 09:37:42,934] [INFO] Running command: blastn -query GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8812b7c-69b0-4a12-929a-e347ea7ba624/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:43,920] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:43,924] [INFO] Selected 9 target genomes.
[2023-06-05 09:37:43,924] [INFO] Target genome list was writen to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:37:43,932] [INFO] Task started: fastANI
[2023-06-05 09:37:43,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f5ef0c4-ab63-404b-ae86-e04e3b59d899/GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna.gz --refList GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/target_genomes_gtdb.txt --output GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:37:51,486] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:51,500] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:37:51,501] [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_900215325.1	s__Fibrobacter sp900215325	97.5445	861	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.50	97.09	0.94	0.94	6	conclusive
GCF_900177805.1	s__Fibrobacter sp900177805	91.6792	780	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.22	97.22	0.89	0.89	2	-
GCA_902791475.1	s__Fibrobacter succinogenes_J	91.4542	736	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.39	95.39	0.76	0.76	2	-
GCF_000146505.1	s__Fibrobacter succinogenes	91.439	760	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002210425.1	s__Fibrobacter elongatus	91.4359	778	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.37	97.19	0.91	0.89	4	-
GCA_002394865.1	s__Fibrobacter sp002394865	90.2669	746	912	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	89.6822	754	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.16	96.29	0.89	0.80	6	-
GCF_900143015.1	s__Fibrobacter sp900143015	87.1861	733	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.36	97.36	0.90	0.90	2	-
GCA_902776765.1	s__Fibrobacter succinogenes_N	85.5409	687	912	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:37:51,503] [INFO] GTDB search result was written to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/result_gtdb.tsv
[2023-06-05 09:37:51,503] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:37:51,506] [INFO] DFAST_QC result json was written to GCA_902758405.1_Rumen_uncultured_genome_RUG10364_genomic.fna/dqc_result.json
[2023-06-05 09:37:51,506] [INFO] DFAST_QC completed!
[2023-06-05 09:37:51,506] [INFO] Total running time: 0h1m1s