[2023-06-07 23:26:41,487] [INFO] DFAST_QC pipeline started.
[2023-06-07 23:26:41,488] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 23:26:41,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference
[2023-06-07 23:26:43,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 23:26:43,890] [INFO] Task started: Prodigal
[2023-06-07 23:26:43,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd2123ec-23bc-4180-9e91-9ac22eca8f80/GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna.gz | prodigal -d GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/cds.fna -a GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 23:27:03,300] [INFO] Task succeeded: Prodigal
[2023-06-07 23:27:03,301] [INFO] Task started: HMMsearch
[2023-06-07 23:27:03,301] [INFO] Running command: hmmsearch --tblout GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/reference_markers.hmm GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/protein.faa > /dev/null
[2023-06-07 23:27:03,564] [INFO] Task succeeded: HMMsearch
[2023-06-07 23:27:03,565] [INFO] Found 6/6 markers.
[2023-06-07 23:27:03,596] [INFO] Query marker FASTA was written to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/markers.fasta
[2023-06-07 23:27:03,596] [INFO] Task started: Blastn
[2023-06-07 23:27:03,596] [INFO] Running command: blastn -query GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/markers.fasta -db /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/reference_markers.fasta -out GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:27:04,210] [INFO] Task succeeded: Blastn
[2023-06-07 23:27:04,216] [INFO] Selected 30 target genomes.
[2023-06-07 23:27:04,216] [INFO] Target genome list was writen to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/target_genomes.txt
[2023-06-07 23:27:04,244] [INFO] Task started: fastANI
[2023-06-07 23:27:04,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd2123ec-23bc-4180-9e91-9ac22eca8f80/GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna.gz --refList GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/target_genomes.txt --output GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 23:27:18,497] [INFO] Task succeeded: fastANI
[2023-06-07 23:27:18,498] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 23:27:18,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 23:27:18,506] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 23:27:18,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 23:27:18,506] [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
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.541	61	1016	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.1846	96	1016	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.1737	94	1016	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.092	94	1016	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	75.8917	69	1016	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	75.8791	66	1016	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	75.7485	55	1016	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	75.7485	55	1016	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 23:27:18,508] [INFO] DFAST Taxonomy check result was written to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/tc_result.tsv
[2023-06-07 23:27:18,509] [INFO] ===== Taxonomy check completed =====
[2023-06-07 23:27:18,509] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 23:27:18,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/checkm_data
[2023-06-07 23:27:18,510] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 23:27:18,548] [INFO] Task started: CheckM
[2023-06-07 23:27:18,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/checkm_input GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/checkm_result
[2023-06-07 23:28:13,575] [INFO] Task succeeded: CheckM
[2023-06-07 23:28:13,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 23:28:13,597] [INFO] ===== Completeness check finished =====
[2023-06-07 23:28:13,597] [INFO] ===== Start GTDB Search =====
[2023-06-07 23:28:13,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/markers.fasta)
[2023-06-07 23:28:13,598] [INFO] Task started: Blastn
[2023-06-07 23:28:13,598] [INFO] Running command: blastn -query GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/markers.fasta -db /var/lib/cwl/stgf12959d9-ebe6-4690-9b7f-cfcd6cec2d7a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 23:28:14,555] [INFO] Task succeeded: Blastn
[2023-06-07 23:28:14,559] [INFO] Selected 12 target genomes.
[2023-06-07 23:28:14,559] [INFO] Target genome list was writen to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 23:28:14,562] [INFO] Task started: fastANI
[2023-06-07 23:28:14,562] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd2123ec-23bc-4180-9e91-9ac22eca8f80/GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna.gz --refList GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/target_genomes_gtdb.txt --output GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 23:28:24,001] [INFO] Task succeeded: fastANI
[2023-06-07 23:28:24,013] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 23:28:24,013] [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_902799985.1	s__UBA4372 sp902799985	97.7512	761	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.87	97.87	0.82	0.82	2	conclusive
GCA_002394305.1	s__UBA4372 sp002394305	88.4852	618	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.13	97.13	0.80	0.80	2	-
GCA_017483665.1	s__UBA4372 sp017483665	87.3427	642	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776455.1	s__UBA4372 sp902776455	83.676	598	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.21	96.34	0.88	0.83	6	-
GCA_900313705.1	s__UBA4372 sp900313705	83.5946	543	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	97.31	96.93	0.85	0.79	9	-
GCA_902763865.1	s__UBA4372 sp902763865	81.705	513	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.22	98.22	0.85	0.84	3	-
GCA_017541265.1	s__UBA4372 sp017541265	81.6053	516	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428785.1	s__UBA4372 sp017428785	81.4274	483	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.90	96.90	0.83	0.83	2	-
GCA_017469525.1	s__UBA4372 sp017469525	81.1728	515	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	98.07	96.85	0.89	0.86	4	-
GCA_902779315.1	s__UBA4372 sp902779315	79.9682	395	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	96.37	95.96	0.89	0.85	5	-
GCA_905235305.1	s__UBA4372 sp905235305	79.9328	387	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017552435.1	s__UBA4372 sp017552435	79.098	426	1016	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 23:28:24,015] [INFO] GTDB search result was written to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/result_gtdb.tsv
[2023-06-07 23:28:24,016] [INFO] ===== GTDB Search completed =====
[2023-06-07 23:28:24,019] [INFO] DFAST_QC result json was written to GCA_902800565.1_Rumen_uncultured_genome_RUG14587_genomic.fna/dqc_result.json
[2023-06-07 23:28:24,019] [INFO] DFAST_QC completed!
[2023-06-07 23:28:24,019] [INFO] Total running time: 0h1m43s