[2023-06-08 18:05:31,808] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:05:31,811] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:05:31,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference
[2023-06-08 18:05:33,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:05:33,969] [INFO] Task started: Prodigal
[2023-06-08 18:05:33,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg5752f51c-b132-468e-8658-0cef14d2cde8/GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna.gz | prodigal -d GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/cds.fna -a GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:05:45,311] [INFO] Task succeeded: Prodigal
[2023-06-08 18:05:45,311] [INFO] Task started: HMMsearch
[2023-06-08 18:05:45,312] [INFO] Running command: hmmsearch --tblout GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/reference_markers.hmm GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:05:45,572] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:05:45,574] [INFO] Found 6/6 markers.
[2023-06-08 18:05:45,599] [INFO] Query marker FASTA was written to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/markers.fasta
[2023-06-08 18:05:45,600] [INFO] Task started: Blastn
[2023-06-08 18:05:45,600] [INFO] Running command: blastn -query GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/markers.fasta -db /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/reference_markers.fasta -out GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:05:46,228] [INFO] Task succeeded: Blastn
[2023-06-08 18:05:46,235] [INFO] Selected 25 target genomes.
[2023-06-08 18:05:46,236] [INFO] Target genome list was writen to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/target_genomes.txt
[2023-06-08 18:05:46,241] [INFO] Task started: fastANI
[2023-06-08 18:05:46,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg5752f51c-b132-468e-8658-0cef14d2cde8/GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna.gz --refList GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/target_genomes.txt --output GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:05:57,560] [INFO] Task succeeded: fastANI
[2023-06-08 18:05:57,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:05:57,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:05:57,576] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:05:57,576] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 18:05:57,576] [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	78.2357	122	751	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.7682	79	751	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.6849	78	751	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.675	78	751	95	below_threshold
Prevotella melaninogenica	strain=FDAARGOS_1566	GCA_020735785.1	28132	28132	suspected-type	True	77.5316	64	751	95	below_threshold
Prevotella melaninogenica	strain=ATCC 25845	GCA_000144405.1	28132	28132	suspected-type	True	77.4898	63	751	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.4265	103	751	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.4217	68	751	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.3721	104	751	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	77.236	56	751	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.1572	67	751	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.0123	56	751	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.8989	56	751	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.857	56	751	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.7966	71	751	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.71	63	751	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.242	65	751	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.2104	63	751	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.1991	62	751	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 18:05:57,579] [INFO] DFAST Taxonomy check result was written to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/tc_result.tsv
[2023-06-08 18:05:57,579] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:05:57,580] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:05:57,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/checkm_data
[2023-06-08 18:05:57,582] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:05:57,614] [INFO] Task started: CheckM
[2023-06-08 18:05:57,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/checkm_input GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/checkm_result
[2023-06-08 18:06:34,116] [INFO] Task succeeded: CheckM
[2023-06-08 18:06:34,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:06:34,136] [INFO] ===== Completeness check finished =====
[2023-06-08 18:06:34,136] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:06:34,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/markers.fasta)
[2023-06-08 18:06:34,137] [INFO] Task started: Blastn
[2023-06-08 18:06:34,137] [INFO] Running command: blastn -query GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/markers.fasta -db /var/lib/cwl/stg721842f3-958a-4204-86a4-a2d554f4757c/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:06:35,018] [INFO] Task succeeded: Blastn
[2023-06-08 18:06:35,022] [INFO] Selected 25 target genomes.
[2023-06-08 18:06:35,022] [INFO] Target genome list was writen to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:06:35,030] [INFO] Task started: fastANI
[2023-06-08 18:06:35,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg5752f51c-b132-468e-8658-0cef14d2cde8/GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna.gz --refList GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/target_genomes_gtdb.txt --output GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:06:47,103] [INFO] Task succeeded: fastANI
[2023-06-08 18:06:47,134] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:06:47,134] [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_900315775.1	s__Prevotella sp900315775	97.3756	654	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.72	95.29	0.88	0.81	29	conclusive
GCA_017449725.1	s__Prevotella sp017449725	79.6278	263	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.06	97.95	0.63	0.62	3	-
GCA_002394385.1	s__Prevotella sp002394385	77.9809	160	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.28	97.06	0.88	0.86	9	-
GCF_900110895.1	s__Prevotella sp900110895	77.8594	95	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.50	96.66	0.93	0.90	3	-
GCA_016291495.1	s__Prevotella sp016291495	77.7702	109	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799905.1	s__Prevotella sp902799905	77.7547	113	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCA_900199555.1	s__Prevotella sp900199555	77.7486	126	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.82	97.80	0.89	0.85	3	-
GCA_017412705.1	s__Prevotella sp017412705	77.7273	122	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554105.1	s__Prevotella sp017554105	77.7015	142	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315095.1	s__Prevotella sp900315095	77.6964	153	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.59	96.16	0.90	0.86	18	-
GCA_002379425.1	s__Prevotella sp002379425	77.5543	73	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000834015.1	s__Prevotella pectinovora	77.3721	104	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_900320445.1	s__Prevotella sp900320445	77.2909	120	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.78	96.58	0.88	0.79	4	-
GCA_002353205.1	s__Prevotella sp002353205	77.2506	101	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.92	99.92	0.98	0.98	2	-
GCA_902780025.1	s__Prevotella sp902780025	77.2184	121	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761905.1	s__Prevotella sp902761905	77.1926	115	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900079775.1	s__Prevotella lascolaii	77.1572	67	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	98.20	0.94	0.92	5	-
GCA_900544495.1	s__Prevotella sp900544495	77.0277	90	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_017550455.1	s__Prevotella sp017550455	76.9583	86	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.76	0.76	2	-
GCA_902774815.1	s__Prevotella sp902774815	76.9363	91	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342415.1	s__Prevotella sp002342415	76.933	109	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	76.8511	74	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCA_002395135.1	s__Prevotella sp002395135	76.8333	78	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.98	98.98	0.83	0.83	2	-
GCA_017635615.1	s__Prevotella sp017635615	76.4547	77	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797505.1	s__Prevotella sp902797505	76.2791	77	751	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.08	95.72	0.78	0.72	7	-
--------------------------------------------------------------------------------
[2023-06-08 18:06:47,136] [INFO] GTDB search result was written to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/result_gtdb.tsv
[2023-06-08 18:06:47,137] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:06:47,142] [INFO] DFAST_QC result json was written to GCA_902800405.1_Rumen_uncultured_genome_RUG14567_genomic.fna/dqc_result.json
[2023-06-08 18:06:47,142] [INFO] DFAST_QC completed!
[2023-06-08 18:06:47,142] [INFO] Total running time: 0h1m15s