[2023-06-04 20:01:54,758] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:01:54,760] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:01:54,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference
[2023-06-04 20:01:56,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:01:56,081] [INFO] Task started: Prodigal
[2023-06-04 20:01:56,082] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e28dfaa-95c1-4a32-84eb-a0e81d4feb2f/GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna.gz | prodigal -d GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/cds.fna -a GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:02:07,743] [INFO] Task succeeded: Prodigal
[2023-06-04 20:02:07,744] [INFO] Task started: HMMsearch
[2023-06-04 20:02:07,744] [INFO] Running command: hmmsearch --tblout GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/reference_markers.hmm GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:02:07,968] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:02:07,970] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6e28dfaa-95c1-4a32-84eb-a0e81d4feb2f/GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna.gz]
[2023-06-04 20:02:07,999] [INFO] Query marker FASTA was written to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/markers.fasta
[2023-06-04 20:02:08,000] [INFO] Task started: Blastn
[2023-06-04 20:02:08,000] [INFO] Running command: blastn -query GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/reference_markers.fasta -out GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:08,590] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:08,595] [INFO] Selected 16 target genomes.
[2023-06-04 20:02:08,595] [INFO] Target genome list was writen to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/target_genomes.txt
[2023-06-04 20:02:08,597] [INFO] Task started: fastANI
[2023-06-04 20:02:08,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e28dfaa-95c1-4a32-84eb-a0e81d4feb2f/GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna.gz --refList GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/target_genomes.txt --output GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:02:17,103] [INFO] Task succeeded: fastANI
[2023-06-04 20:02:17,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:02:17,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:02:17,118] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 20:02:17,118] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 20:02:17,118] [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 hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	80.9427	289	611	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	80.7993	315	611	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	80.7508	321	611	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	80.6991	313	611	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.7058	83	611	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	77.325	90	611	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.0916	72	611	95	below_threshold
Prevotella herbatica	strain=WR041	GCA_017347605.1	2801997	2801997	type	True	77.0475	60	611	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.9812	103	611	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.977	106	611	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.7674	76	611	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.6772	78	611	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.4577	82	611	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:02:17,121] [INFO] DFAST Taxonomy check result was written to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/tc_result.tsv
[2023-06-04 20:02:17,122] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:02:17,122] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:02:17,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/checkm_data
[2023-06-04 20:02:17,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:02:17,153] [INFO] Task started: CheckM
[2023-06-04 20:02:17,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/checkm_input GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/checkm_result
[2023-06-04 20:02:54,635] [INFO] Task succeeded: CheckM
[2023-06-04 20:02:54,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:02:54,661] [INFO] ===== Completeness check finished =====
[2023-06-04 20:02:54,661] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:02:54,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/markers.fasta)
[2023-06-04 20:02:54,662] [INFO] Task started: Blastn
[2023-06-04 20:02:54,662] [INFO] Running command: blastn -query GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ebd4683-72f4-442e-bec2-b15bea426be6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:02:55,468] [INFO] Task succeeded: Blastn
[2023-06-04 20:02:55,473] [INFO] Selected 9 target genomes.
[2023-06-04 20:02:55,473] [INFO] Target genome list was writen to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:02:55,516] [INFO] Task started: fastANI
[2023-06-04 20:02:55,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e28dfaa-95c1-4a32-84eb-a0e81d4feb2f/GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna.gz --refList GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/target_genomes_gtdb.txt --output GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:03:01,006] [INFO] Task succeeded: fastANI
[2023-06-04 20:03:01,023] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:03:01,023] [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
GCF_009495355.1	s__Prevotella sp900313215	97.617	498	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.34	96.92	0.81	0.74	15	conclusive
GCA_900556395.1	s__Prevotella sp900556395	85.4001	404	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.81	0.83	0.82	3	-
GCA_002439605.1	s__Prevotella sp002439605	85.1092	383	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.57	99.57	0.81	0.81	2	-
GCF_000157935.1	s__Prevotella copri	80.8174	314	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCF_015074785.1	s__Prevotella sp015074785	80.7636	314	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_002297965.1	s__Prevotella sp002297965	80.2663	256	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.14	99.14	0.78	0.78	2	-
GCA_900555035.1	s__Prevotella sp900555035	80.2551	264	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436035.1	s__Prevotella sp000436035	80.1658	295	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCA_900548535.1	s__Prevotella sp900548535	79.7663	292	611	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 20:03:01,026] [INFO] GTDB search result was written to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/result_gtdb.tsv
[2023-06-04 20:03:01,028] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:03:01,033] [INFO] DFAST_QC result json was written to GCA_902782025.1_Rumen_uncultured_genome_RUG12728_genomic.fna/dqc_result.json
[2023-06-04 20:03:01,033] [INFO] DFAST_QC completed!
[2023-06-04 20:03:01,033] [INFO] Total running time: 0h1m6s