[2023-06-05 04:28:09,146] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:28:09,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:28:09,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference
[2023-06-05 04:28:11,057] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:28:11,058] [INFO] Task started: Prodigal
[2023-06-05 04:28:11,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg5662b0de-bc20-4ce4-8bce-942eae2f79ea/GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna.gz | prodigal -d GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/cds.fna -a GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:28:20,387] [INFO] Task succeeded: Prodigal
[2023-06-05 04:28:20,388] [INFO] Task started: HMMsearch
[2023-06-05 04:28:20,388] [INFO] Running command: hmmsearch --tblout GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/reference_markers.hmm GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:28:20,732] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:28:20,734] [INFO] Found 6/6 markers.
[2023-06-05 04:28:20,783] [INFO] Query marker FASTA was written to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/markers.fasta
[2023-06-05 04:28:20,784] [INFO] Task started: Blastn
[2023-06-05 04:28:20,784] [INFO] Running command: blastn -query GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/reference_markers.fasta -out GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:28:21,573] [INFO] Task succeeded: Blastn
[2023-06-05 04:28:21,593] [INFO] Selected 24 target genomes.
[2023-06-05 04:28:21,594] [INFO] Target genome list was writen to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/target_genomes.txt
[2023-06-05 04:28:21,642] [INFO] Task started: fastANI
[2023-06-05 04:28:21,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg5662b0de-bc20-4ce4-8bce-942eae2f79ea/GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna.gz --refList GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/target_genomes.txt --output GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:28:43,185] [INFO] Task succeeded: fastANI
[2023-06-05 04:28:43,186] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:28:43,187] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:28:43,197] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:28:43,197] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:28:43,198] [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	80.0225	447	1078	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	79.9698	448	1078	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.321	156	1078	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	77.0292	64	1078	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:28:43,200] [INFO] DFAST Taxonomy check result was written to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/tc_result.tsv
[2023-06-05 04:28:43,201] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:28:43,201] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:28:43,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/checkm_data
[2023-06-05 04:28:43,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:28:43,263] [INFO] Task started: CheckM
[2023-06-05 04:28:43,263] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/checkm_input GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/checkm_result
[2023-06-05 04:29:14,786] [INFO] Task succeeded: CheckM
[2023-06-05 04:29:14,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.38%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:29:14,813] [INFO] ===== Completeness check finished =====
[2023-06-05 04:29:14,813] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:29:14,813] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/markers.fasta)
[2023-06-05 04:29:14,814] [INFO] Task started: Blastn
[2023-06-05 04:29:14,814] [INFO] Running command: blastn -query GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a344fb-464d-4f54-b1c1-8d155234d0c8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:29:15,979] [INFO] Task succeeded: Blastn
[2023-06-05 04:29:15,983] [INFO] Selected 9 target genomes.
[2023-06-05 04:29:15,983] [INFO] Target genome list was writen to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:29:15,990] [INFO] Task started: fastANI
[2023-06-05 04:29:15,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg5662b0de-bc20-4ce4-8bce-942eae2f79ea/GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna.gz --refList GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/target_genomes_gtdb.txt --output GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:29:22,772] [INFO] Task succeeded: fastANI
[2023-06-05 04:29:22,787] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:29:22,788] [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_902771595.1	s__Fibrobacter succinogenes_C	100.0	1067	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.72	98.72	0.91	0.91	2	conclusive
GCA_017551775.1	s__Fibrobacter sp017551775	94.6231	842	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762305.1	s__Fibrobacter succinogenes_I	91.462	873	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210285.1	s__Fibrobacter sp002210285	86.3678	777	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.84	95.65	0.91	0.85	4	-
GCF_900143055.1	s__Fibrobacter sp900143055	84.6579	715	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.51	95.61	0.84	0.74	8	-
GCA_002449765.1	s__Fibrobacter sp002449765	84.3636	670	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.21	96.54	0.93	0.89	8	-
GCA_902800815.1	s__Fibrobacter succinogenes_B	84.2205	665	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.10	97.10	0.90	0.90	2	-
GCA_017642335.1	s__Fibrobacter sp017642335	82.7901	575	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.30	98.30	0.90	0.90	2	-
GCA_902781185.1	s__Fibrobacter succinogenes_G	80.6127	290	1078	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.40	96.40	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-05 04:29:22,791] [INFO] GTDB search result was written to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/result_gtdb.tsv
[2023-06-05 04:29:22,792] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:29:22,796] [INFO] DFAST_QC result json was written to GCA_902771595.1_Rumen_uncultured_genome_RUG11683_genomic.fna/dqc_result.json
[2023-06-05 04:29:22,796] [INFO] DFAST_QC completed!
[2023-06-05 04:29:22,796] [INFO] Total running time: 0h1m14s