[2023-06-07 20:07:52,799] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:07:52,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:07:52,802] [INFO] DQC Reference Directory: /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference
[2023-06-07 20:07:54,838] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:07:54,839] [INFO] Task started: Prodigal
[2023-06-07 20:07:54,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a61d225-ae72-486d-9ee7-07220b1a338a/GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna.gz | prodigal -d GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/cds.fna -a GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:08:03,555] [INFO] Task succeeded: Prodigal
[2023-06-07 20:08:03,555] [INFO] Task started: HMMsearch
[2023-06-07 20:08:03,555] [INFO] Running command: hmmsearch --tblout GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/reference_markers.hmm GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:08:03,810] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:08:03,811] [INFO] Found 6/6 markers.
[2023-06-07 20:08:03,840] [INFO] Query marker FASTA was written to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/markers.fasta
[2023-06-07 20:08:03,840] [INFO] Task started: Blastn
[2023-06-07 20:08:03,840] [INFO] Running command: blastn -query GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/markers.fasta -db /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/reference_markers.fasta -out GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:04,430] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:04,434] [INFO] Selected 15 target genomes.
[2023-06-07 20:08:04,435] [INFO] Target genome list was writen to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/target_genomes.txt
[2023-06-07 20:08:04,439] [INFO] Task started: fastANI
[2023-06-07 20:08:04,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a61d225-ae72-486d-9ee7-07220b1a338a/GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna.gz --refList GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/target_genomes.txt --output GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:08:14,813] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:14,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:08:14,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:08:14,820] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:08:14,820] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:08:14,820] [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	80.0821	411	1007	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	80.0101	407	1007	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.9605	153	1007	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	77.1153	63	1007	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:08:14,822] [INFO] DFAST Taxonomy check result was written to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/tc_result.tsv
[2023-06-07 20:08:14,823] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:08:14,823] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:08:14,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/checkm_data
[2023-06-07 20:08:14,824] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:08:14,862] [INFO] Task started: CheckM
[2023-06-07 20:08:14,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/checkm_input GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/checkm_result
[2023-06-07 20:08:45,549] [INFO] Task succeeded: CheckM
[2023-06-07 20:08:45,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 8.33%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-07 20:08:45,573] [INFO] ===== Completeness check finished =====
[2023-06-07 20:08:45,573] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:08:45,573] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/markers.fasta)
[2023-06-07 20:08:45,574] [INFO] Task started: Blastn
[2023-06-07 20:08:45,574] [INFO] Running command: blastn -query GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/markers.fasta -db /var/lib/cwl/stgea820bdf-4cec-4c5e-ba23-0da51d14b2b6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:46,353] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:46,357] [INFO] Selected 14 target genomes.
[2023-06-07 20:08:46,357] [INFO] Target genome list was writen to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:08:46,362] [INFO] Task started: fastANI
[2023-06-07 20:08:46,362] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a61d225-ae72-486d-9ee7-07220b1a338a/GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna.gz --refList GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/target_genomes_gtdb.txt --output GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:08:56,639] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:56,655] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 20:08:56,655] [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_017526585.1	s__Fibrobacter sp017526585	94.4595	758	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799745.1	s__Fibrobacter succinogenes_Q	85.0772	589	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210295.1	s__Fibrobacter sp002210295	84.9923	644	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142545.1	s__Fibrobacter sp900142545	84.9207	657	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902756345.1	s__Fibrobacter sp900142495	84.7807	638	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.15	97.22	0.91	0.83	8	-
GCA_900316465.1	s__Fibrobacter sp900316465	84.7504	615	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142475.1	s__Fibrobacter sp900142475	84.5645	651	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.25	95.07	0.84	0.80	4	-
GCF_900177705.1	s__Fibrobacter sp900177705	84.5528	637	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.87	99.82	0.99	0.99	3	-
GCA_902794535.1	s__Fibrobacter succinogenes_O	84.5504	616	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603905.1	s__Fibrobacter sp001603905	84.5418	611	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.67	95.34	0.91	0.84	3	-
GCA_017530965.1	s__Fibrobacter sp017530965	84.1628	551	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761355.1	s__Fibrobacter succinogenes_M	83.952	562	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550445.1	s__Fibrobacter sp017550445	82.5456	581	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143055.1	s__Fibrobacter sp900143055	81.6881	492	1007	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.51	95.61	0.84	0.74	8	-
--------------------------------------------------------------------------------
[2023-06-07 20:08:56,658] [INFO] GTDB search result was written to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/result_gtdb.tsv
[2023-06-07 20:08:56,659] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:08:56,663] [INFO] DFAST_QC result json was written to GCA_902793175.1_Rumen_uncultured_genome_RUG13847_genomic.fna/dqc_result.json
[2023-06-07 20:08:56,663] [INFO] DFAST_QC completed!
[2023-06-07 20:08:56,663] [INFO] Total running time: 0h1m4s