[2023-06-05 14:48:16,251] [INFO] DFAST_QC pipeline started.
[2023-06-05 14:48:16,254] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 14:48:16,255] [INFO] DQC Reference Directory: /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference
[2023-06-05 14:48:17,828] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 14:48:17,829] [INFO] Task started: Prodigal
[2023-06-05 14:48:17,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b576a5e-89b0-4631-9b9e-88ff13ff22ae/GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna.gz | prodigal -d GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/cds.fna -a GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 14:48:29,095] [INFO] Task succeeded: Prodigal
[2023-06-05 14:48:29,096] [INFO] Task started: HMMsearch
[2023-06-05 14:48:29,096] [INFO] Running command: hmmsearch --tblout GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/reference_markers.hmm GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/protein.faa > /dev/null
[2023-06-05 14:48:29,272] [INFO] Task succeeded: HMMsearch
[2023-06-05 14:48:29,273] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b576a5e-89b0-4631-9b9e-88ff13ff22ae/GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna.gz]
[2023-06-05 14:48:29,293] [INFO] Query marker FASTA was written to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/markers.fasta
[2023-06-05 14:48:29,294] [INFO] Task started: Blastn
[2023-06-05 14:48:29,294] [INFO] Running command: blastn -query GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/markers.fasta -db /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/reference_markers.fasta -out GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:48:29,832] [INFO] Task succeeded: Blastn
[2023-06-05 14:48:29,836] [INFO] Selected 25 target genomes.
[2023-06-05 14:48:29,836] [INFO] Target genome list was writen to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/target_genomes.txt
[2023-06-05 14:48:29,838] [INFO] Task started: fastANI
[2023-06-05 14:48:29,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b576a5e-89b0-4631-9b9e-88ff13ff22ae/GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna.gz --refList GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/target_genomes.txt --output GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 14:48:43,592] [INFO] Task succeeded: fastANI
[2023-06-05 14:48:43,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 14:48:43,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 14:48:43,601] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 14:48:43,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 14:48:43,601] [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 stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.3491	126	729	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.234	121	729	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	77.1609	128	729	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.7613	129	729	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.757	103	729	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.6787	106	729	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.6315	119	729	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.6306	98	729	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.4817	56	729	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.4653	75	729	95	below_threshold
Prevotella multisaccharivorax	strain=DSM 17128	GCA_000218235.1	310514	310514	type	True	76.4471	59	729	95	below_threshold
Prevotella multisaccharivorax	strain=JCM 12954	GCA_019973315.1	310514	310514	type	True	76.4158	60	729	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 14:48:43,605] [INFO] DFAST Taxonomy check result was written to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/tc_result.tsv
[2023-06-05 14:48:43,606] [INFO] ===== Taxonomy check completed =====
[2023-06-05 14:48:43,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 14:48:43,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/checkm_data
[2023-06-05 14:48:43,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 14:48:43,633] [INFO] Task started: CheckM
[2023-06-05 14:48:43,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/checkm_input GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/checkm_result
[2023-06-05 14:49:17,502] [INFO] Task succeeded: CheckM
[2023-06-05 14:49:17,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 2.60%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-05 14:49:17,522] [INFO] ===== Completeness check finished =====
[2023-06-05 14:49:17,522] [INFO] ===== Start GTDB Search =====
[2023-06-05 14:49:17,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/markers.fasta)
[2023-06-05 14:49:17,523] [INFO] Task started: Blastn
[2023-06-05 14:49:17,523] [INFO] Running command: blastn -query GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/markers.fasta -db /var/lib/cwl/stgdee2b0dc-6af2-49ab-a411-0408b6e7b2ac/dqc_reference/reference_markers_gtdb.fasta -out GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 14:49:18,318] [INFO] Task succeeded: Blastn
[2023-06-05 14:49:18,321] [INFO] Selected 23 target genomes.
[2023-06-05 14:49:18,321] [INFO] Target genome list was writen to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 14:49:18,333] [INFO] Task started: fastANI
[2023-06-05 14:49:18,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b576a5e-89b0-4631-9b9e-88ff13ff22ae/GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna.gz --refList GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/target_genomes_gtdb.txt --output GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 14:49:31,048] [INFO] Task succeeded: fastANI
[2023-06-05 14:49:31,062] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 14:49:31,062] [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_900318625.1	s__Prevotella sp900318625	97.4025	617	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.03	0.86	0.78	43	conclusive
GCA_002353555.1	s__Prevotella sp002353555	78.2828	146	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.61	97.57	0.79	0.77	3	-
GCA_902771785.1	s__Prevotella sp902771785	77.736	162	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.01	98.01	0.87	0.87	2	-
GCA_002353205.1	s__Prevotella sp002353205	77.5644	161	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.92	99.92	0.98	0.98	2	-
GCA_902776685.1	s__Prevotella sp902776685	77.556	160	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	77.555	191	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_017557185.1	s__Prevotella sp017557185	77.3457	149	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019052365.1	s__Prevotella sp000434975	77.2122	134	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCA_002392835.1	s__Prevotella sp002392835	77.1803	137	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.57	97.57	0.74	0.74	2	-
GCA_905233425.1	s__Prevotella sp905233425	77.1085	163	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767045.1	s__Prevotella sp902767045	77.0829	141	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.95	96.95	0.81	0.81	2	-
GCF_002251435.1	s__Prevotella sp002251435	76.9854	73	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615355.1	s__Prevotella sp017615355	76.9853	115	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353525.1	s__Prevotella sp002353525	76.9748	126	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547005.1	s__Prevotella sp900547005	76.9432	113	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.66	96.14	0.84	0.69	4	-
GCA_900318685.1	s__Prevotella sp900318685	76.9123	122	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	97.52	0.91	0.84	4	-
GCA_017442765.1	s__Prevotella sp017442765	76.8691	130	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905196835.1	s__Prevotella stercoripullorum	76.865	124	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_902792685.1	s__Prevotella sp902792685	76.8459	93	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.79	96.68	0.73	0.71	4	-
GCA_900315455.1	s__Prevotella sp900315455	76.8171	136	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCF_000426585.1	s__Prevotella baroniae	76.757	103	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.01	0.95	0.92	4	-
GCA_905198745.1	s__Prevotella sp905198745	76.4941	87	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373605.1	s__Prevotella sp905373605	76.1296	60	729	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 14:49:31,064] [INFO] GTDB search result was written to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/result_gtdb.tsv
[2023-06-05 14:49:31,064] [INFO] ===== GTDB Search completed =====
[2023-06-05 14:49:31,069] [INFO] DFAST_QC result json was written to GCA_902771895.1_Rumen_uncultured_genome_RUG11709_genomic.fna/dqc_result.json
[2023-06-05 14:49:31,069] [INFO] DFAST_QC completed!
[2023-06-05 14:49:31,069] [INFO] Total running time: 0h1m15s