[2023-06-08 05:33:32,865] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:32,882] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:32,882] [INFO] DQC Reference Directory: /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference
[2023-06-08 05:33:35,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:35,711] [INFO] Task started: Prodigal
[2023-06-08 05:33:35,711] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6f222db-0cde-4252-b5f8-e92eec21fade/GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna.gz | prodigal -d GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/cds.fna -a GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:33:54,066] [INFO] Task succeeded: Prodigal
[2023-06-08 05:33:54,066] [INFO] Task started: HMMsearch
[2023-06-08 05:33:54,066] [INFO] Running command: hmmsearch --tblout GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/reference_markers.hmm GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:33:54,316] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:33:54,317] [INFO] Found 6/6 markers.
[2023-06-08 05:33:54,349] [INFO] Query marker FASTA was written to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/markers.fasta
[2023-06-08 05:33:54,350] [INFO] Task started: Blastn
[2023-06-08 05:33:54,350] [INFO] Running command: blastn -query GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/reference_markers.fasta -out GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:54,952] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:54,956] [INFO] Selected 24 target genomes.
[2023-06-08 05:33:54,957] [INFO] Target genome list was writen to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/target_genomes.txt
[2023-06-08 05:33:54,958] [INFO] Task started: fastANI
[2023-06-08 05:33:54,958] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f222db-0cde-4252-b5f8-e92eec21fade/GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna.gz --refList GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/target_genomes.txt --output GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:34:06,603] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:06,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:34:06,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:34:06,619] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:34:06,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:34:06,620] [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 brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.1811	206	1067	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.3937	231	1067	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.3729	230	1067	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.12	195	1067	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.0737	201	1067	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0439	141	1067	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.0228	207	1067	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.971	121	1067	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.5715	117	1067	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.5315	100	1067	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.4975	118	1067	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.4734	65	1067	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4696	97	1067	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.2873	87	1067	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.1915	141	1067	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	76.0906	80	1067	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.0745	81	1067	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	75.6908	59	1067	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:34:06,622] [INFO] DFAST Taxonomy check result was written to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/tc_result.tsv
[2023-06-08 05:34:06,623] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:34:06,623] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:34:06,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/checkm_data
[2023-06-08 05:34:06,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:34:06,662] [INFO] Task started: CheckM
[2023-06-08 05:34:06,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/checkm_input GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/checkm_result
[2023-06-08 05:34:59,665] [INFO] Task succeeded: CheckM
[2023-06-08 05:34:59,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:34:59,691] [INFO] ===== Completeness check finished =====
[2023-06-08 05:34:59,691] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:34:59,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/markers.fasta)
[2023-06-08 05:34:59,692] [INFO] Task started: Blastn
[2023-06-08 05:34:59,692] [INFO] Running command: blastn -query GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/markers.fasta -db /var/lib/cwl/stg36c35072-3a5e-4a4e-acaa-16e381ac63ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:35:00,638] [INFO] Task succeeded: Blastn
[2023-06-08 05:35:00,643] [INFO] Selected 13 target genomes.
[2023-06-08 05:35:00,643] [INFO] Target genome list was writen to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:35:00,644] [INFO] Task started: fastANI
[2023-06-08 05:35:00,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6f222db-0cde-4252-b5f8-e92eec21fade/GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna.gz --refList GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/target_genomes_gtdb.txt --output GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:35:09,325] [INFO] Task succeeded: fastANI
[2023-06-08 05:35:09,342] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:35:09,342] [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_902800435.1	s__Prevotella sp902800435	100.0	1061	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.98	95.98	0.77	0.77	2	conclusive
GCA_017395215.1	s__Prevotella sp017395215	92.594	629	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235325.1	s__Prevotella sp905235325	87.9034	554	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316475.1	s__Prevotella sp900316475	81.9941	487	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.70	97.71	0.86	0.81	4	-
GCA_902780025.1	s__Prevotella sp902780025	81.6754	521	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800495.1	s__Prevotella sp902800495	81.5916	462	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321965.1	s__Prevotella sp900321965	81.5344	439	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016285245.1	s__Prevotella sp016285245	80.909	416	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	80.4246	494	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_902794405.1	s__Prevotella sp902794405	80.3335	457	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545045.1	s__Prevotella sp017545045	79.823	313	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449025.1	s__Prevotella sp017449025	79.2907	334	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702825.1	s__Prevotella sp000702825	77.4941	219	1067	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.44	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-08 05:35:09,354] [INFO] GTDB search result was written to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/result_gtdb.tsv
[2023-06-08 05:35:09,354] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:35:09,359] [INFO] DFAST_QC result json was written to GCA_902800435.1_Rumen_uncultured_genome_RUG14572_genomic.fna/dqc_result.json
[2023-06-08 05:35:09,359] [INFO] DFAST_QC completed!
[2023-06-08 05:35:09,359] [INFO] Total running time: 0h1m36s