[2023-06-05 11:11:57,377] [INFO] DFAST_QC pipeline started.
[2023-06-05 11:11:57,382] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 11:11:57,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference
[2023-06-05 11:11:59,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 11:11:59,604] [INFO] Task started: Prodigal
[2023-06-05 11:11:59,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg609bb411-6b52-410f-99a1-453179bdee0b/GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna.gz | prodigal -d GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/cds.fna -a GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 11:12:16,775] [INFO] Task succeeded: Prodigal
[2023-06-05 11:12:16,776] [INFO] Task started: HMMsearch
[2023-06-05 11:12:16,776] [INFO] Running command: hmmsearch --tblout GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/reference_markers.hmm GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/protein.faa > /dev/null
[2023-06-05 11:12:17,040] [INFO] Task succeeded: HMMsearch
[2023-06-05 11:12:17,042] [INFO] Found 6/6 markers.
[2023-06-05 11:12:17,070] [INFO] Query marker FASTA was written to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/markers.fasta
[2023-06-05 11:12:17,070] [INFO] Task started: Blastn
[2023-06-05 11:12:17,070] [INFO] Running command: blastn -query GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/reference_markers.fasta -out GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:12:17,652] [INFO] Task succeeded: Blastn
[2023-06-05 11:12:17,657] [INFO] Selected 29 target genomes.
[2023-06-05 11:12:17,658] [INFO] Target genome list was writen to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/target_genomes.txt
[2023-06-05 11:12:17,660] [INFO] Task started: fastANI
[2023-06-05 11:12:17,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg609bb411-6b52-410f-99a1-453179bdee0b/GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna.gz --refList GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/target_genomes.txt --output GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 11:12:33,163] [INFO] Task succeeded: fastANI
[2023-06-05 11:12:33,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 11:12:33,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 11:12:33,178] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 11:12:33,179] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 11:12:33,179] [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 ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.6382	251	959	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.5888	249	959	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.4749	170	959	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.7822	103	959	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.7356	107	959	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5252	78	959	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.4155	85	959	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.2976	56	959	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.2955	55	959	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.1253	56	959	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 11:12:33,181] [INFO] DFAST Taxonomy check result was written to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/tc_result.tsv
[2023-06-05 11:12:33,181] [INFO] ===== Taxonomy check completed =====
[2023-06-05 11:12:33,181] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 11:12:33,182] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/checkm_data
[2023-06-05 11:12:33,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 11:12:33,213] [INFO] Task started: CheckM
[2023-06-05 11:12:33,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/checkm_input GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/checkm_result
[2023-06-05 11:13:24,338] [INFO] Task succeeded: CheckM
[2023-06-05 11:13:24,340] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.40%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 11:13:24,362] [INFO] ===== Completeness check finished =====
[2023-06-05 11:13:24,362] [INFO] ===== Start GTDB Search =====
[2023-06-05 11:13:24,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/markers.fasta)
[2023-06-05 11:13:24,363] [INFO] Task started: Blastn
[2023-06-05 11:13:24,363] [INFO] Running command: blastn -query GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/markers.fasta -db /var/lib/cwl/stg92f7645d-a8cb-44ec-bb4b-3f483cbae87c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 11:13:25,200] [INFO] Task succeeded: Blastn
[2023-06-05 11:13:25,205] [INFO] Selected 13 target genomes.
[2023-06-05 11:13:25,205] [INFO] Target genome list was writen to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 11:13:25,212] [INFO] Task started: fastANI
[2023-06-05 11:13:25,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg609bb411-6b52-410f-99a1-453179bdee0b/GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna.gz --refList GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/target_genomes_gtdb.txt --output GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 11:13:34,314] [INFO] Task succeeded: fastANI
[2023-06-05 11:13:34,330] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 11:13:34,331] [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_902774925.1	s__Prevotella sp902774925	98.7127	840	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	98.74	0.87	0.87	2	conclusive
GCA_900318885.1	s__Prevotella sp900318885	93.288	711	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_902800245.1	s__Prevotella sp902800245	92.5534	731	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318555.1	s__Prevotella sp900318555	92.4168	724	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	96.13	0.85	0.78	8	-
GCA_017447515.1	s__Prevotella sp017447515	86.1822	445	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772585.1	s__Prevotella sp902772585	81.1665	360	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291085.1	s__Prevotella sp016291085	81.0212	514	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902764705.1	s__Prevotella sp902764705	80.8637	474	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800925.1	s__Prevotella sp902800925	80.7275	328	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314985.1	s__Prevotella sp900314985	79.8643	336	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_017449495.1	s__Prevotella sp017449495	78.7211	167	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017965475.1	s__Prevotella sp017965475	78.6796	213	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320255.1	s__Prevotella sp900320255	77.4178	212	959	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	97.73	0.87	0.76	7	-
--------------------------------------------------------------------------------
[2023-06-05 11:13:34,333] [INFO] GTDB search result was written to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/result_gtdb.tsv
[2023-06-05 11:13:34,333] [INFO] ===== GTDB Search completed =====
[2023-06-05 11:13:34,337] [INFO] DFAST_QC result json was written to GCA_902768455.1_Rumen_uncultured_genome_RUG11364_genomic.fna/dqc_result.json
[2023-06-05 11:13:34,337] [INFO] DFAST_QC completed!
[2023-06-05 11:13:34,337] [INFO] Total running time: 0h1m37s