[2023-06-08 11:16:33,212] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:16:33,222] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:16:33,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference
[2023-06-08 11:16:34,631] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:34,632] [INFO] Task started: Prodigal
[2023-06-08 11:16:34,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c2ff0fb-ff8c-486b-b75f-5f386edd5fc1/GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna.gz | prodigal -d GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/cds.fna -a GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:50,360] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:50,360] [INFO] Task started: HMMsearch
[2023-06-08 11:16:50,360] [INFO] Running command: hmmsearch --tblout GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/reference_markers.hmm GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:50,723] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:50,724] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5c2ff0fb-ff8c-486b-b75f-5f386edd5fc1/GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna.gz]
[2023-06-08 11:16:50,761] [INFO] Query marker FASTA was written to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/markers.fasta
[2023-06-08 11:16:50,762] [INFO] Task started: Blastn
[2023-06-08 11:16:50,762] [INFO] Running command: blastn -query GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/markers.fasta -db /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/reference_markers.fasta -out GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:51,405] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:51,412] [INFO] Selected 24 target genomes.
[2023-06-08 11:16:51,412] [INFO] Target genome list was writen to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/target_genomes.txt
[2023-06-08 11:16:51,414] [INFO] Task started: fastANI
[2023-06-08 11:16:51,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c2ff0fb-ff8c-486b-b75f-5f386edd5fc1/GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna.gz --refList GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/target_genomes.txt --output GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:17:02,966] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:02,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:17:02,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:17:02,985] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:17:02,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:17:02,985] [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	78.4476	221	869	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.3492	223	869	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	78.0046	217	869	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.3259	60	869	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.176	82	869	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.0316	57	869	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	75.8644	53	869	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	75.8577	66	869	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	75.8552	55	869	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	75.8311	64	869	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	75.6841	64	869	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	75.6524	56	869	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	75.6524	56	869	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:17:02,987] [INFO] DFAST Taxonomy check result was written to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/tc_result.tsv
[2023-06-08 11:17:02,988] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:17:02,988] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:17:02,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/checkm_data
[2023-06-08 11:17:02,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:17:03,023] [INFO] Task started: CheckM
[2023-06-08 11:17:03,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/checkm_input GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/checkm_result
[2023-06-08 11:17:49,714] [INFO] Task succeeded: CheckM
[2023-06-08 11:17:49,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 11:17:49,737] [INFO] ===== Completeness check finished =====
[2023-06-08 11:17:49,737] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:17:49,737] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/markers.fasta)
[2023-06-08 11:17:49,738] [INFO] Task started: Blastn
[2023-06-08 11:17:49,738] [INFO] Running command: blastn -query GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/markers.fasta -db /var/lib/cwl/stgdacf1fe5-47c2-4a06-8964-84d9316bb88c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:17:50,555] [INFO] Task succeeded: Blastn
[2023-06-08 11:17:50,560] [INFO] Selected 11 target genomes.
[2023-06-08 11:17:50,560] [INFO] Target genome list was writen to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:17:50,566] [INFO] Task started: fastANI
[2023-06-08 11:17:50,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c2ff0fb-ff8c-486b-b75f-5f386edd5fc1/GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna.gz --refList GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/target_genomes_gtdb.txt --output GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:17:58,632] [INFO] Task succeeded: fastANI
[2023-06-08 11:17:58,644] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 11:17:58,645] [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_902800925.1	s__Prevotella sp902800925	100.0	866	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902772585.1	s__Prevotella sp902772585	85.576	556	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799355.1	s__Prevotella sp902799355	85.3293	513	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.80	96.48	0.80	0.78	3	-
GCA_900316265.1	s__Prevotella sp900316265	85.3261	558	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.64	96.94	0.80	0.66	12	-
GCA_900314985.1	s__Prevotella sp900314985	83.5198	543	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_900313235.1	s__Prevotella sp900313235	83.3922	441	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902798425.1	s__Prevotella sp902798425	82.5315	501	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.06	97.06	0.85	0.85	2	-
GCA_900318555.1	s__Prevotella sp900318555	80.2167	339	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	96.13	0.85	0.78	8	-
GCA_900318885.1	s__Prevotella sp900318885	80.1907	337	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_902760345.1	s__Prevotella sp902760345	80.1863	400	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.76	97.90	0.82	0.74	7	-
GCA_900315105.1	s__Prevotella sp900315105	76.7784	85	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
--------------------------------------------------------------------------------
[2023-06-08 11:17:58,647] [INFO] GTDB search result was written to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/result_gtdb.tsv
[2023-06-08 11:17:58,652] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:17:58,655] [INFO] DFAST_QC result json was written to GCA_902800925.1_Rumen_uncultured_genome_RUG14617_genomic.fna/dqc_result.json
[2023-06-08 11:17:58,655] [INFO] DFAST_QC completed!
[2023-06-08 11:17:58,656] [INFO] Total running time: 0h1m25s