[2023-06-05 12:00:32,976] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:00:32,978] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:00:32,978] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference
[2023-06-05 12:00:34,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:00:34,303] [INFO] Task started: Prodigal
[2023-06-05 12:00:34,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8cfeed8-b5ff-4b6f-9816-c122a767ee67/GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna.gz | prodigal -d GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/cds.fna -a GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:00:55,553] [INFO] Task succeeded: Prodigal
[2023-06-05 12:00:55,553] [INFO] Task started: HMMsearch
[2023-06-05 12:00:55,553] [INFO] Running command: hmmsearch --tblout GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/reference_markers.hmm GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:00:55,819] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:00:55,820] [INFO] Found 6/6 markers.
[2023-06-05 12:00:55,860] [INFO] Query marker FASTA was written to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/markers.fasta
[2023-06-05 12:00:55,861] [INFO] Task started: Blastn
[2023-06-05 12:00:55,861] [INFO] Running command: blastn -query GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/reference_markers.fasta -out GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:00:56,509] [INFO] Task succeeded: Blastn
[2023-06-05 12:00:56,513] [INFO] Selected 29 target genomes.
[2023-06-05 12:00:56,513] [INFO] Target genome list was writen to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/target_genomes.txt
[2023-06-05 12:00:56,515] [INFO] Task started: fastANI
[2023-06-05 12:00:56,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8cfeed8-b5ff-4b6f-9816-c122a767ee67/GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna.gz --refList GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/target_genomes.txt --output GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:01:11,037] [INFO] Task succeeded: fastANI
[2023-06-05 12:01:11,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:01:11,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:01:11,052] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:01:11,052] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:01:11,052] [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	78.2791	320	1274	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.2395	320	1274	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.2268	195	1274	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6706	88	1274	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.5641	74	1274	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.5165	98	1274	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4921	103	1274	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.4241	98	1274	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4026	97	1274	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.378	98	1274	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.2685	77	1274	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.1253	107	1274	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	75.7226	57	1274	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	75.7	58	1274	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:01:11,054] [INFO] DFAST Taxonomy check result was written to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/tc_result.tsv
[2023-06-05 12:01:11,055] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:01:11,055] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:01:11,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/checkm_data
[2023-06-05 12:01:11,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:01:11,095] [INFO] Task started: CheckM
[2023-06-05 12:01:11,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/checkm_input GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/checkm_result
[2023-06-05 12:02:11,577] [INFO] Task succeeded: CheckM
[2023-06-05 12:02:11,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.68%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 12:02:11,597] [INFO] ===== Completeness check finished =====
[2023-06-05 12:02:11,597] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:02:11,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/markers.fasta)
[2023-06-05 12:02:11,597] [INFO] Task started: Blastn
[2023-06-05 12:02:11,598] [INFO] Running command: blastn -query GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9d8a965-45ef-4910-944a-95527a03023f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:02:12,484] [INFO] Task succeeded: Blastn
[2023-06-05 12:02:12,488] [INFO] Selected 12 target genomes.
[2023-06-05 12:02:12,488] [INFO] Target genome list was writen to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:02:12,495] [INFO] Task started: fastANI
[2023-06-05 12:02:12,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8cfeed8-b5ff-4b6f-9816-c122a767ee67/GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna.gz --refList GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/target_genomes_gtdb.txt --output GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:02:21,586] [INFO] Task succeeded: fastANI
[2023-06-05 12:02:21,597] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:02:21,597] [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_900316445.1	s__Prevotella sp900316445	100.0	1264	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_017428805.1	s__Prevotella sp017428805	94.452	746	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776545.1	s__Prevotella sp902776545	90.6882	871	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.23	97.16	0.83	0.82	3	-
GCA_016284635.1	s__Prevotella sp016284635	89.044	678	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474845.1	s__Prevotella sp017474845	87.0387	412	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319715.1	s__Prevotella sp900319715	84.2582	650	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	97.29	0.85	0.78	10	-
GCA_016286585.1	s__Prevotella sp016286585	82.4131	580	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449495.1	s__Prevotella sp017449495	82.2472	412	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460765.1	s__Prevotella sp017460765	79.8168	392	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315525.1	s__Prevotella sp900315525	79.3839	415	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.00	0.84	0.76	10	-
GCA_015060485.1	s__Prevotella sp015060485	78.3667	322	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316005.1	s__Prevotella sp002316005	75.7541	52	1274	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:02:21,600] [INFO] GTDB search result was written to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/result_gtdb.tsv
[2023-06-05 12:02:21,600] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:02:21,604] [INFO] DFAST_QC result json was written to GCA_902758285.1_Rumen_uncultured_genome_RUG10346_genomic.fna/dqc_result.json
[2023-06-05 12:02:21,604] [INFO] DFAST_QC completed!
[2023-06-05 12:02:21,604] [INFO] Total running time: 0h1m49s