[2023-06-05 13:30:05,725] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:30:05,728] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:30:05,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference
[2023-06-05 13:30:07,156] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:30:07,157] [INFO] Task started: Prodigal
[2023-06-05 13:30:07,157] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe30c3d6-3d32-4c19-951f-9ee36ac670ad/GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna.gz | prodigal -d GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/cds.fna -a GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:30:11,615] [INFO] Task succeeded: Prodigal
[2023-06-05 13:30:11,615] [INFO] Task started: HMMsearch
[2023-06-05 13:30:11,615] [INFO] Running command: hmmsearch --tblout GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/reference_markers.hmm GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:30:11,805] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:30:11,806] [INFO] Found 6/6 markers.
[2023-06-05 13:30:11,826] [INFO] Query marker FASTA was written to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/markers.fasta
[2023-06-05 13:30:11,826] [INFO] Task started: Blastn
[2023-06-05 13:30:11,826] [INFO] Running command: blastn -query GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/markers.fasta -db /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/reference_markers.fasta -out GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:12,371] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:12,374] [INFO] Selected 23 target genomes.
[2023-06-05 13:30:12,374] [INFO] Target genome list was writen to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/target_genomes.txt
[2023-06-05 13:30:12,380] [INFO] Task started: fastANI
[2023-06-05 13:30:12,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe30c3d6-3d32-4c19-951f-9ee36ac670ad/GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna.gz --refList GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/target_genomes.txt --output GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:30:25,786] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:25,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:30:25,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:30:25,792] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:30:25,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 13:30:25,792] [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
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.7264	128	577	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	76.9647	111	577	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	76.7893	55	577	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	76.7364	88	577	95	below_threshold
Mailhella massiliensis	strain=Marseille-P3199	GCA_900155525.1	1903261	1903261	type	True	76.5193	58	577	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 13:30:25,794] [INFO] DFAST Taxonomy check result was written to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/tc_result.tsv
[2023-06-05 13:30:25,795] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:30:25,795] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:30:25,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/checkm_data
[2023-06-05 13:30:25,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:30:25,823] [INFO] Task started: CheckM
[2023-06-05 13:30:25,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/checkm_input GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/checkm_result
[2023-06-05 13:30:44,149] [INFO] Task succeeded: CheckM
[2023-06-05 13:30:44,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:30:44,168] [INFO] ===== Completeness check finished =====
[2023-06-05 13:30:44,168] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:30:44,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/markers.fasta)
[2023-06-05 13:30:44,169] [INFO] Task started: Blastn
[2023-06-05 13:30:44,169] [INFO] Running command: blastn -query GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/markers.fasta -db /var/lib/cwl/stg324c6503-9812-4424-98f2-8dc97f53e61e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:30:45,012] [INFO] Task succeeded: Blastn
[2023-06-05 13:30:45,016] [INFO] Selected 15 target genomes.
[2023-06-05 13:30:45,016] [INFO] Target genome list was writen to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:30:45,025] [INFO] Task started: fastANI
[2023-06-05 13:30:45,026] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe30c3d6-3d32-4c19-951f-9ee36ac670ad/GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna.gz --refList GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/target_genomes_gtdb.txt --output GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:30:52,632] [INFO] Task succeeded: fastANI
[2023-06-05 13:30:52,641] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:30:52,641] [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_900319575.1	s__Desulfovibrio sp900319575	98.1549	448	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	98.58	98.15	0.89	0.78	8	conclusive
GCA_900546145.1	s__Desulfovibrio sp900546145	94.7231	536	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.05	98.98	0.92	0.90	3	-
GCA_002369295.1	s__Desulfovibrio sp002369295	78.9611	196	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.45	99.45	0.84	0.84	2	-
GCA_016284885.1	s__Desulfovibrio sp016284885	78.7544	203	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.92	95.09	0.88	0.83	3	-
GCA_019113165.1	s__Desulfovibrio intestinipullorum	77.9139	158	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156375.1	s__Desulfovibrio piger	77.7264	128	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCF_900116045.1	s__Desulfovibrio piger_A	77.5099	139	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCA_019118745.1	s__Desulfovibrio gallistercoris	77.3382	106	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159665.1	s__Desulfovibrio faecigallinarum	77.3216	123	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	98.21	97.37	0.93	0.87	4	-
GCA_019118345.1	s__Desulfovibrio intestinavium	77.0731	91	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215675.1	s__Desulfovibrio sp905215675	76.8935	80	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001553605.1	s__Desulfovibrio fairfieldensis	76.7052	116	577	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	-
--------------------------------------------------------------------------------
[2023-06-05 13:30:52,644] [INFO] GTDB search result was written to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/result_gtdb.tsv
[2023-06-05 13:30:52,646] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:30:52,650] [INFO] DFAST_QC result json was written to GCA_902782015.1_Rumen_uncultured_genome_RUG12731_genomic.fna/dqc_result.json
[2023-06-05 13:30:52,650] [INFO] DFAST_QC completed!
[2023-06-05 13:30:52,650] [INFO] Total running time: 0h0m47s