[2023-06-05 18:27:00,315] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:27:00,320] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:27:00,320] [INFO] DQC Reference Directory: /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference
[2023-06-05 18:27:01,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:27:01,733] [INFO] Task started: Prodigal
[2023-06-05 18:27:01,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg25765839-2d95-42c8-ae2c-cccadb5233ca/GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna.gz | prodigal -d GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/cds.fna -a GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:27:15,002] [INFO] Task succeeded: Prodigal
[2023-06-05 18:27:15,003] [INFO] Task started: HMMsearch
[2023-06-05 18:27:15,003] [INFO] Running command: hmmsearch --tblout GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/reference_markers.hmm GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:27:15,214] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:27:15,216] [INFO] Found 6/6 markers.
[2023-06-05 18:27:15,240] [INFO] Query marker FASTA was written to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/markers.fasta
[2023-06-05 18:27:15,241] [INFO] Task started: Blastn
[2023-06-05 18:27:15,241] [INFO] Running command: blastn -query GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/reference_markers.fasta -out GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:27:15,783] [INFO] Task succeeded: Blastn
[2023-06-05 18:27:15,787] [INFO] Selected 19 target genomes.
[2023-06-05 18:27:15,788] [INFO] Target genome list was writen to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/target_genomes.txt
[2023-06-05 18:27:15,788] [INFO] Task started: fastANI
[2023-06-05 18:27:15,789] [INFO] Running command: fastANI --query /var/lib/cwl/stg25765839-2d95-42c8-ae2c-cccadb5233ca/GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna.gz --refList GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/target_genomes.txt --output GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:27:25,755] [INFO] Task succeeded: fastANI
[2023-06-05 18:27:25,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:27:25,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:27:25,762] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:27:25,762] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:27:25,762] [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	79.7828	313	936	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.2157	263	936	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.1486	266	936	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.1861	76	936	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.5994	83	936	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.3471	85	936	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.257	71	936	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.1474	74	936	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	75.9736	66	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:27:25,764] [INFO] DFAST Taxonomy check result was written to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/tc_result.tsv
[2023-06-05 18:27:25,765] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:27:25,765] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:27:25,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/checkm_data
[2023-06-05 18:27:25,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:27:25,796] [INFO] Task started: CheckM
[2023-06-05 18:27:25,796] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/checkm_input GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/checkm_result
[2023-06-05 18:28:07,521] [INFO] Task succeeded: CheckM
[2023-06-05 18:28:07,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:28:07,549] [INFO] ===== Completeness check finished =====
[2023-06-05 18:28:07,549] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:28:07,552] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/markers.fasta)
[2023-06-05 18:28:07,552] [INFO] Task started: Blastn
[2023-06-05 18:28:07,552] [INFO] Running command: blastn -query GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/markers.fasta -db /var/lib/cwl/stg81f9db47-3ec2-4549-a38d-8542f85df3a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:28:08,437] [INFO] Task succeeded: Blastn
[2023-06-05 18:28:08,444] [INFO] Selected 12 target genomes.
[2023-06-05 18:28:08,444] [INFO] Target genome list was writen to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:28:08,445] [INFO] Task started: fastANI
[2023-06-05 18:28:08,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg25765839-2d95-42c8-ae2c-cccadb5233ca/GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna.gz --refList GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/target_genomes_gtdb.txt --output GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:28:17,282] [INFO] Task succeeded: fastANI
[2023-06-05 18:28:17,291] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:28:17,292] [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_900100635.1	s__Prevotella sp900100635	96.9779	810	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	conclusive
GCA_902799975.1	s__Prevotella sp902799975	82.6869	532	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778255.1	s__Prevotella sp902778255	82.5372	536	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.79	0.87	0.87	2	-
GCA_902788605.1	s__Prevotella sp902788605	81.5091	443	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_902785695.1	s__Prevotella sp902785695	80.8761	365	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775605.1	s__Prevotella sp902775605	80.6031	373	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799905.1	s__Prevotella sp902799905	79.3478	346	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_017483805.1	s__Prevotella sp017483805	78.6081	315	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900199555.1	s__Prevotella sp900199555	78.5903	227	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.80	0.89	0.85	3	-
GCA_902800495.1	s__Prevotella sp902800495	78.0058	227	936	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	77.939	228	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017474925.1	s__Prevotella sp017474925	77.6558	105	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.19	98.19	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:28:17,295] [INFO] GTDB search result was written to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/result_gtdb.tsv
[2023-06-05 18:28:17,296] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:28:17,299] [INFO] DFAST_QC result json was written to GCA_902781995.1_Rumen_uncultured_genome_RUG12729_genomic.fna/dqc_result.json
[2023-06-05 18:28:17,300] [INFO] DFAST_QC completed!
[2023-06-05 18:28:17,300] [INFO] Total running time: 0h1m17s