[2023-06-05 18:56:51,843] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:56:51,846] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:56:51,846] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference
[2023-06-05 18:56:53,874] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:56:53,875] [INFO] Task started: Prodigal
[2023-06-05 18:56:53,875] [INFO] Running command: gunzip -c /var/lib/cwl/stga4bd5a9a-90ba-4877-ba6b-e6cb21d72b88/GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna.gz | prodigal -d GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/cds.fna -a GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:23,911] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:23,912] [INFO] Task started: HMMsearch
[2023-06-05 18:57:23,912] [INFO] Running command: hmmsearch --tblout GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/reference_markers.hmm GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:24,292] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:24,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga4bd5a9a-90ba-4877-ba6b-e6cb21d72b88/GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna.gz]
[2023-06-05 18:57:24,338] [INFO] Query marker FASTA was written to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/markers.fasta
[2023-06-05 18:57:24,339] [INFO] Task started: Blastn
[2023-06-05 18:57:24,339] [INFO] Running command: blastn -query GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/reference_markers.fasta -out GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:24,988] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:24,992] [INFO] Selected 25 target genomes.
[2023-06-05 18:57:24,992] [INFO] Target genome list was writen to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/target_genomes.txt
[2023-06-05 18:57:24,993] [INFO] Task started: fastANI
[2023-06-05 18:57:24,994] [INFO] Running command: fastANI --query /var/lib/cwl/stga4bd5a9a-90ba-4877-ba6b-e6cb21d72b88/GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna.gz --refList GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/target_genomes.txt --output GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:38,852] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:38,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:38,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:38,871] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:38,871] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:57:38,871] [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	77.8896	197	1147	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.3675	166	1147	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	77.1513	123	1147	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	77.1016	89	1147	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	77.0741	90	1147	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	77.0725	176	1147	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0662	159	1147	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.9852	132	1147	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.9519	134	1147	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.9135	174	1147	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.8844	176	1147	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.7863	130	1147	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7013	132	1147	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.6587	81	1147	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.5884	86	1147	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.5708	87	1147	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.5524	93	1147	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.527	125	1147	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.453	95	1147	95	below_threshold
Prevotella bergensis	strain=DSM 17361	GCA_000160535.1	242750	242750	type	True	76.145	82	1147	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:57:38,875] [INFO] DFAST Taxonomy check result was written to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/tc_result.tsv
[2023-06-05 18:57:38,877] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:38,877] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:38,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/checkm_data
[2023-06-05 18:57:38,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:38,950] [INFO] Task started: CheckM
[2023-06-05 18:57:38,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/checkm_input GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/checkm_result
[2023-06-05 18:58:41,893] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:41,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:41,918] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:41,918] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:41,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/markers.fasta)
[2023-06-05 18:58:41,919] [INFO] Task started: Blastn
[2023-06-05 18:58:41,919] [INFO] Running command: blastn -query GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ae9020e-8cb0-44e4-8ef0-d6a9ad6530cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:42,822] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:42,827] [INFO] Selected 26 target genomes.
[2023-06-05 18:58:42,827] [INFO] Target genome list was writen to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:42,838] [INFO] Task started: fastANI
[2023-06-05 18:58:42,839] [INFO] Running command: fastANI --query /var/lib/cwl/stga4bd5a9a-90ba-4877-ba6b-e6cb21d72b88/GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna.gz --refList GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/target_genomes_gtdb.txt --output GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:58,816] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:58,840] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:58:58,841] [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_002350805.1	s__Prevotella sp002350805	98.1941	723	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.30	97.51	0.83	0.79	8	conclusive
GCA_002353525.1	s__Prevotella sp002353525	84.7248	528	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788605.1	s__Prevotella sp902788605	81.9107	207	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_016291595.1	s__Prevotella sp016291595	81.894	516	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442765.1	s__Prevotella sp017442765	79.1354	148	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781315.1	s__Prevotella sp902781315	78.8427	291	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_900315565.1	s__Prevotella sp900315565	78.8308	364	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.12	96.25	0.91	0.84	3	-
GCA_017619445.1	s__Prevotella sp017619445	78.6548	273	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314655.1	s__Prevotella sp900314655	78.1286	251	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	95.82	0.85	0.71	9	-
GCA_017508965.1	s__Prevotella sp017508965	78.0853	224	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.39	95.39	0.73	0.73	2	-
GCA_902775975.1	s__Prevotella sp902775975	78.073	163	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCF_900110085.1	s__Prevotella sp900110085	78.027	218	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.82	0.82	3	-
GCA_900318395.1	s__Prevotella sp900318395	77.9977	199	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.69	96.89	0.88	0.81	6	-
GCA_900316285.1	s__Prevotella sp900316285	77.8738	283	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.02	95.37	0.87	0.79	21	-
GCA_900316985.1	s__Prevotella sp900316985	77.8502	241	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.04	0.81	0.71	7	-
GCA_902784755.1	s__Prevotella sp902784755	77.8388	142	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.59	97.59	0.83	0.83	2	-
GCA_002394385.1	s__Prevotella sp002394385	77.7599	212	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCA_902799905.1	s__Prevotella sp902799905	77.7052	205	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_900318885.1	s__Prevotella sp900318885	77.6275	186	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_002363695.1	s__Prevotella sp002363695	77.5224	141	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017400455.1	s__Prevotella sp017400455	77.4927	205	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557405.1	s__Prevotella sp017557405	77.4233	201	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018789675.1	s__Prevotella sp002300055	77.066	159	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.15	99.02	0.92	0.90	6	-
GCA_002437285.1	s__Prevotella sp002437285	76.8962	150	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.68	99.38	0.93	0.88	13	-
GCA_900555035.1	s__Prevotella sp900555035	76.8292	90	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290275.1	s__Prevotella sp900290275	76.3296	75	1147	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.80	97.71	0.90	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:58,843] [INFO] GTDB search result was written to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:58,843] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:58,848] [INFO] DFAST_QC result json was written to GCA_902791005.1_Rumen_uncultured_genome_RUG13624_genomic.fna/dqc_result.json
[2023-06-05 18:58:58,848] [INFO] DFAST_QC completed!
[2023-06-05 18:58:58,849] [INFO] Total running time: 0h2m7s