[2023-06-05 12:34:02,542] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:34:02,544] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:34:02,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference
[2023-06-05 12:34:03,748] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:34:03,749] [INFO] Task started: Prodigal
[2023-06-05 12:34:03,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg2596fee1-df14-47d3-8c29-4418bc5854ef/GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna.gz | prodigal -d GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/cds.fna -a GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:34:29,326] [INFO] Task succeeded: Prodigal
[2023-06-05 12:34:29,327] [INFO] Task started: HMMsearch
[2023-06-05 12:34:29,327] [INFO] Running command: hmmsearch --tblout GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/reference_markers.hmm GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:34:29,631] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:34:29,633] [INFO] Found 6/6 markers.
[2023-06-05 12:34:29,673] [INFO] Query marker FASTA was written to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/markers.fasta
[2023-06-05 12:34:29,674] [INFO] Task started: Blastn
[2023-06-05 12:34:29,674] [INFO] Running command: blastn -query GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/markers.fasta -db /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/reference_markers.fasta -out GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:34:30,300] [INFO] Task succeeded: Blastn
[2023-06-05 12:34:30,305] [INFO] Selected 29 target genomes.
[2023-06-05 12:34:30,306] [INFO] Target genome list was writen to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/target_genomes.txt
[2023-06-05 12:34:30,307] [INFO] Task started: fastANI
[2023-06-05 12:34:30,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg2596fee1-df14-47d3-8c29-4418bc5854ef/GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna.gz --refList GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/target_genomes.txt --output GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:34:45,888] [INFO] Task succeeded: fastANI
[2023-06-05 12:34:45,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:34:45,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:34:45,907] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:34:45,907] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:34:45,907] [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 koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	77.0443	51	1330	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	76.7527	69	1330	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.6562	81	1330	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.6505	103	1330	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	76.6159	134	1330	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.5103	117	1330	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.5083	117	1330	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.479	94	1330	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4542	128	1330	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	76.4441	70	1330	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.4164	119	1330	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.3907	77	1330	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.3886	120	1330	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.3741	120	1330	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.3718	79	1330	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.3554	120	1330	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.3546	73	1330	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.1401	90	1330	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:34:45,912] [INFO] DFAST Taxonomy check result was written to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/tc_result.tsv
[2023-06-05 12:34:45,912] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:34:45,913] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:34:45,913] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/checkm_data
[2023-06-05 12:34:45,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:34:45,975] [INFO] Task started: CheckM
[2023-06-05 12:34:45,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/checkm_input GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/checkm_result
[2023-06-05 12:35:57,907] [INFO] Task succeeded: CheckM
[2023-06-05 12:35:57,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:35:57,932] [INFO] ===== Completeness check finished =====
[2023-06-05 12:35:57,933] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:35:57,934] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/markers.fasta)
[2023-06-05 12:35:57,935] [INFO] Task started: Blastn
[2023-06-05 12:35:57,935] [INFO] Running command: blastn -query GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/markers.fasta -db /var/lib/cwl/stg23ba1e60-23ec-4fb9-a6f0-b473c7acdeed/dqc_reference/reference_markers_gtdb.fasta -out GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:35:58,793] [INFO] Task succeeded: Blastn
[2023-06-05 12:35:58,798] [INFO] Selected 19 target genomes.
[2023-06-05 12:35:58,799] [INFO] Target genome list was writen to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:35:58,807] [INFO] Task started: fastANI
[2023-06-05 12:35:58,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg2596fee1-df14-47d3-8c29-4418bc5854ef/GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna.gz --refList GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/target_genomes_gtdb.txt --output GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:36:11,876] [INFO] Task succeeded: fastANI
[2023-06-05 12:36:11,895] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:36:11,895] [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_902780635.1	s__Prevotella sp902780635	100.0	1329	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	97.41	0.85	0.85	2	conclusive
GCA_902767775.1	s__Prevotella sp902767775	79.2401	480	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.97	97.97	0.86	0.86	2	-
GCA_900317305.1	s__Prevotella sp900317305	79.1246	422	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.38	97.82	0.87	0.83	11	-
GCA_902776475.1	s__Prevotella sp902776475	79.0549	457	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.89	97.89	0.91	0.91	2	-
GCA_900320585.1	s__Prevotella sp900320585	79.0065	411	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.77	98.44	0.87	0.81	6	-
GCA_900315455.1	s__Prevotella sp900315455	78.9017	443	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.41	96.59	0.90	0.86	13	-
GCA_016281815.1	s__Prevotella sp016281815	78.7055	421	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961115.1	s__Prevotella sp017961115	78.6425	378	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786665.1	s__Prevotella sp902786665	78.5214	447	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.72	98.72	0.89	0.89	2	-
GCA_017617615.1	s__Prevotella sp017617615	78.436	282	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792855.1	s__Prevotella sp902792855	78.1654	382	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.67	98.62	0.88	0.82	4	-
GCA_900315075.1	s__Prevotella sp900315075	77.7768	328	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.96	98.41	0.92	0.87	4	-
GCA_017548385.1	s__Prevotella sp017548385	77.6141	214	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235975.1	s__Prevotella sp905235975	77.2434	166	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017538105.1	s__Prevotella sp017538105	76.8704	214	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025925.1	s__Prevotella ruminicola	76.5103	117	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.74	96.82	0.88	0.80	15	-
GCA_900762125.1	s__Prevotella sp900762125	76.4427	105	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518545.1	s__Prevotella seregens	76.4044	119	1330	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.68	98.64	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-05 12:36:11,897] [INFO] GTDB search result was written to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/result_gtdb.tsv
[2023-06-05 12:36:11,898] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:36:11,902] [INFO] DFAST_QC result json was written to GCA_902780635.1_Rumen_uncultured_genome_RUG12596_genomic.fna/dqc_result.json
[2023-06-05 12:36:11,902] [INFO] DFAST_QC completed!
[2023-06-05 12:36:11,903] [INFO] Total running time: 0h2m9s