[2023-06-05 18:52:27,676] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:52:27,679] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:52:27,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference
[2023-06-05 18:52:28,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:52:28,826] [INFO] Task started: Prodigal
[2023-06-05 18:52:28,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg29e3f795-0d5c-4a8a-974e-e11d2fdaedef/GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna.gz | prodigal -d GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/cds.fna -a GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:52:42,476] [INFO] Task succeeded: Prodigal
[2023-06-05 18:52:42,476] [INFO] Task started: HMMsearch
[2023-06-05 18:52:42,476] [INFO] Running command: hmmsearch --tblout GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/reference_markers.hmm GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:52:42,691] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:52:42,693] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg29e3f795-0d5c-4a8a-974e-e11d2fdaedef/GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna.gz]
[2023-06-05 18:52:42,719] [INFO] Query marker FASTA was written to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/markers.fasta
[2023-06-05 18:52:42,719] [INFO] Task started: Blastn
[2023-06-05 18:52:42,719] [INFO] Running command: blastn -query GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/markers.fasta -db /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/reference_markers.fasta -out GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:52:43,240] [INFO] Task succeeded: Blastn
[2023-06-05 18:52:43,244] [INFO] Selected 14 target genomes.
[2023-06-05 18:52:43,245] [INFO] Target genome list was writen to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/target_genomes.txt
[2023-06-05 18:52:43,245] [INFO] Task started: fastANI
[2023-06-05 18:52:43,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg29e3f795-0d5c-4a8a-974e-e11d2fdaedef/GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna.gz --refList GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/target_genomes.txt --output GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:52:51,557] [INFO] Task succeeded: fastANI
[2023-06-05 18:52:51,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:52:51,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:52:51,565] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:52:51,565] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:52:51,565] [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	78.1966	159	861	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	77.9956	185	861	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.9535	183	861	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	76.8489	58	861	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	76.7699	69	861	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	76.7043	66	861	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.6093	65	861	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.3624	82	861	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	76.3543	79	861	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.2966	83	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:52:51,567] [INFO] DFAST Taxonomy check result was written to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/tc_result.tsv
[2023-06-05 18:52:51,568] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:52:51,568] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:52:51,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/checkm_data
[2023-06-05 18:52:51,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:52:51,597] [INFO] Task started: CheckM
[2023-06-05 18:52:51,598] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/checkm_input GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/checkm_result
[2023-06-05 18:53:36,907] [INFO] Task succeeded: CheckM
[2023-06-05 18:53:36,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.65%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:53:36,923] [INFO] ===== Completeness check finished =====
[2023-06-05 18:53:36,923] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:53:36,924] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/markers.fasta)
[2023-06-05 18:53:36,924] [INFO] Task started: Blastn
[2023-06-05 18:53:36,924] [INFO] Running command: blastn -query GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/markers.fasta -db /var/lib/cwl/stgc124c435-3a68-467b-956e-c71603d375b5/dqc_reference/reference_markers_gtdb.fasta -out GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:53:37,506] [INFO] Task succeeded: Blastn
[2023-06-05 18:53:37,510] [INFO] Selected 15 target genomes.
[2023-06-05 18:53:37,510] [INFO] Target genome list was writen to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:53:37,515] [INFO] Task started: fastANI
[2023-06-05 18:53:37,515] [INFO] Running command: fastANI --query /var/lib/cwl/stg29e3f795-0d5c-4a8a-974e-e11d2fdaedef/GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna.gz --refList GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/target_genomes_gtdb.txt --output GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:53:48,545] [INFO] Task succeeded: fastANI
[2023-06-05 18:53:48,555] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:53:48,555] [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_900318795.1	s__Prevotella sp900318795	96.7149	633	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.54	96.27	0.80	0.72	18	conclusive
GCA_002363695.1	s__Prevotella sp002363695	87.8061	340	861	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	80.9362	440	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107705.1	s__Prevotella sp900107705	80.3365	363	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_017412705.1	s__Prevotella sp017412705	80.3138	392	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353485.1	s__Prevotella sp002353485	79.8587	345	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.45	97.45	0.90	0.90	2	-
GCA_017941345.1	s__Prevotella sp017941345	79.8269	205	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458125.1	s__Prevotella sp017458125	79.8165	373	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.42	97.42	0.81	0.81	2	-
GCA_015060535.1	s__Prevotella sp015060535	79.5131	318	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.13	96.66	0.74	0.70	4	-
GCA_902800925.1	s__Prevotella sp902800925	79.2012	273	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017847725.1	s__Prevotella sp017847725	79.0292	257	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017447515.1	s__Prevotella sp017447515	78.8353	224	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902772585.1	s__Prevotella sp902772585	78.7879	282	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800245.1	s__Prevotella sp902800245	78.7844	316	861	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780025.1	s__Prevotella sp902780025	78.285	236	861	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 18:53:48,558] [INFO] GTDB search result was written to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/result_gtdb.tsv
[2023-06-05 18:53:48,558] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:53:48,561] [INFO] DFAST_QC result json was written to GCA_902758245.1_Rumen_uncultured_genome_RUG10349_genomic.fna/dqc_result.json
[2023-06-05 18:53:48,561] [INFO] DFAST_QC completed!
[2023-06-05 18:53:48,561] [INFO] Total running time: 0h1m21s