[2023-06-07 20:40:02,208] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:02,211] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:02,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference
[2023-06-07 20:40:03,791] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:03,792] [INFO] Task started: Prodigal
[2023-06-07 20:40:03,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eafae06-7cb0-41bf-b19f-fad6eebf10e2/GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna.gz | prodigal -d GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/cds.fna -a GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:23,392] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:23,393] [INFO] Task started: HMMsearch
[2023-06-07 20:40:23,393] [INFO] Running command: hmmsearch --tblout GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/reference_markers.hmm GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:23,679] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:23,681] [INFO] Found 6/6 markers.
[2023-06-07 20:40:23,717] [INFO] Query marker FASTA was written to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/markers.fasta
[2023-06-07 20:40:23,718] [INFO] Task started: Blastn
[2023-06-07 20:40:23,718] [INFO] Running command: blastn -query GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/reference_markers.fasta -out GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:24,380] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:24,384] [INFO] Selected 26 target genomes.
[2023-06-07 20:40:24,384] [INFO] Target genome list was writen to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/target_genomes.txt
[2023-06-07 20:40:24,386] [INFO] Task started: fastANI
[2023-06-07 20:40:24,386] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eafae06-7cb0-41bf-b19f-fad6eebf10e2/GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna.gz --refList GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/target_genomes.txt --output GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:37,348] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:37,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:37,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:37,364] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:37,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:40:37,365] [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	78.8951	183	1029	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	78.4408	240	1029	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	78.4272	236	1029	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6817	82	1029	95	below_threshold
Prevotella fusca	strain=JCM 17724	GCA_000614245.1	589436	589436	type	True	76.3141	53	1029	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.3141	53	1029	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.3141	53	1029	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.3007	63	1029	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2911	76	1029	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	76.2615	83	1029	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.1467	87	1029	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.1168	91	1029	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.115	91	1029	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.0787	70	1029	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.0488	89	1029	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.0422	62	1029	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.0352	65	1029	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.0342	82	1029	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:40:37,367] [INFO] DFAST Taxonomy check result was written to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/tc_result.tsv
[2023-06-07 20:40:37,368] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:37,368] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:37,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/checkm_data
[2023-06-07 20:40:37,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:37,412] [INFO] Task started: CheckM
[2023-06-07 20:40:37,412] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/checkm_input GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/checkm_result
[2023-06-07 20:41:34,019] [INFO] Task succeeded: CheckM
[2023-06-07 20:41:34,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.88%
Contamintation: 15.10%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2023-06-07 20:41:34,047] [INFO] ===== Completeness check finished =====
[2023-06-07 20:41:34,048] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:41:34,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/markers.fasta)
[2023-06-07 20:41:34,049] [INFO] Task started: Blastn
[2023-06-07 20:41:34,049] [INFO] Running command: blastn -query GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b1204f8-6400-44c2-a2c1-e7dfb3040481/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:41:34,893] [INFO] Task succeeded: Blastn
[2023-06-07 20:41:34,898] [INFO] Selected 27 target genomes.
[2023-06-07 20:41:34,898] [INFO] Target genome list was writen to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:41:34,902] [INFO] Task started: fastANI
[2023-06-07 20:41:34,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eafae06-7cb0-41bf-b19f-fad6eebf10e2/GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna.gz --refList GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/target_genomes_gtdb.txt --output GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:41:49,849] [INFO] Task succeeded: fastANI
[2023-06-07 20:41:49,873] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:41:49,873] [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_902760345.1	s__Prevotella sp902760345	98.6128	702	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.76	97.90	0.82	0.74	7	conclusive
GCA_900316265.1	s__Prevotella sp900316265	81.408	394	1029	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	80.5401	434	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.71	97.24	0.86	0.81	12	-
GCA_902772585.1	s__Prevotella sp902772585	80.5362	371	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784065.1	s__Prevotella sp902784065	80.5283	201	1029	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	80.437	393	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.80	96.48	0.80	0.78	3	-
GCA_902800925.1	s__Prevotella sp902800925	80.0433	386	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900313235.1	s__Prevotella sp900313235	79.9965	362	1029	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	79.7619	360	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.06	97.06	0.85	0.85	2	-
GCA_900320045.1	s__Prevotella sp900320045	79.6262	299	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.65	96.17	0.87	0.75	5	-
GCA_902774925.1	s__Prevotella sp902774925	79.5557	367	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.74	98.74	0.87	0.87	2	-
GCA_900318885.1	s__Prevotella sp900318885	79.5098	339	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.27	96.53	0.88	0.77	3	-
GCA_902799975.1	s__Prevotella sp902799975	79.5097	202	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060535.1	s__Prevotella sp015060535	79.4152	338	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.66	0.74	0.70	4	-
GCA_900318555.1	s__Prevotella sp900318555	79.1713	352	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.81	96.13	0.85	0.78	8	-
GCA_016286995.1	s__Prevotella sp016286995	79.1005	306	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775975.1	s__Prevotella sp902775975	79.073	311	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	97.15	0.83	0.83	2	-
GCA_902760315.1	s__Prevotella sp902760315	78.9738	337	1029	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	78.7191	296	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.80	0.89	0.85	3	-
GCA_900315105.1	s__Prevotella sp900315105	78.5834	79	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.64	97.28	0.95	0.91	3	-
GCA_900315695.1	s__Prevotella sp900315695	78.534	215	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.90	97.22	0.82	0.74	6	-
GCA_016291005.1	s__Prevotella sp016291005	78.4373	325	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784615.1	s__Prevotella sp902784615	78.3033	237	1029	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	78.2622	241	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
GCA_900319305.1	s__Prevotella sp900319305	78.2584	209	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.83	97.65	0.87	0.75	3	-
GCA_017483805.1	s__Prevotella sp017483805	78.0022	247	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776545.1	s__Prevotella sp902776545	77.8865	265	1029	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.23	97.16	0.83	0.82	3	-
--------------------------------------------------------------------------------
[2023-06-07 20:41:49,875] [INFO] GTDB search result was written to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/result_gtdb.tsv
[2023-06-07 20:41:49,876] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:41:49,880] [INFO] DFAST_QC result json was written to GCA_902786675.1_Rumen_uncultured_genome_RUG13194_genomic.fna/dqc_result.json
[2023-06-07 20:41:49,881] [INFO] DFAST_QC completed!
[2023-06-07 20:41:49,881] [INFO] Total running time: 0h1m48s