[2023-06-05 00:38:09,964] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:09,966] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:09,966] [INFO] DQC Reference Directory: /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference
[2023-06-05 00:38:11,477] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:11,478] [INFO] Task started: Prodigal
[2023-06-05 00:38:11,478] [INFO] Running command: gunzip -c /var/lib/cwl/stg0297fb1c-e287-43df-bf69-500d4692bf33/GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna.gz | prodigal -d GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/cds.fna -a GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:24,644] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:24,645] [INFO] Task started: HMMsearch
[2023-06-05 00:38:24,645] [INFO] Running command: hmmsearch --tblout GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/reference_markers.hmm GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:24,904] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:24,906] [INFO] Found 6/6 markers.
[2023-06-05 00:38:24,975] [INFO] Query marker FASTA was written to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/markers.fasta
[2023-06-05 00:38:24,976] [INFO] Task started: Blastn
[2023-06-05 00:38:24,976] [INFO] Running command: blastn -query GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/reference_markers.fasta -out GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:25,626] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:25,630] [INFO] Selected 28 target genomes.
[2023-06-05 00:38:25,631] [INFO] Target genome list was writen to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/target_genomes.txt
[2023-06-05 00:38:25,633] [INFO] Task started: fastANI
[2023-06-05 00:38:25,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg0297fb1c-e287-43df-bf69-500d4692bf33/GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna.gz --refList GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/target_genomes.txt --output GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:39,870] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:39,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:39,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:39,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:39,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:38:39,872] [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
--------------------------------------------------------------------------------
[2023-06-05 00:38:39,874] [INFO] DFAST Taxonomy check result was written to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/tc_result.tsv
[2023-06-05 00:38:39,876] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:39,877] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:39,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/checkm_data
[2023-06-05 00:38:39,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:39,910] [INFO] Task started: CheckM
[2023-06-05 00:38:39,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/checkm_input GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/checkm_result
[2023-06-05 00:39:19,960] [INFO] Task succeeded: CheckM
[2023-06-05 00:39:19,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:39:19,982] [INFO] ===== Completeness check finished =====
[2023-06-05 00:39:19,983] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:39:19,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/markers.fasta)
[2023-06-05 00:39:19,984] [INFO] Task started: Blastn
[2023-06-05 00:39:19,984] [INFO] Running command: blastn -query GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/markers.fasta -db /var/lib/cwl/stg78ec2b89-76ed-4a19-8436-555d105ff1ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:39:20,844] [INFO] Task succeeded: Blastn
[2023-06-05 00:39:20,849] [INFO] Selected 23 target genomes.
[2023-06-05 00:39:20,849] [INFO] Target genome list was writen to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:39:20,860] [INFO] Task started: fastANI
[2023-06-05 00:39:20,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg0297fb1c-e287-43df-bf69-500d4692bf33/GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna.gz --refList GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/target_genomes_gtdb.txt --output GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:39:28,944] [INFO] Task succeeded: fastANI
[2023-06-05 00:39:28,974] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:39:28,974] [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_900316005.1	s__RF16 sp900316005	97.1653	613	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.46	95.78	0.88	0.80	13	conclusive
GCA_017509715.1	s__RF16 sp017509715	78.1226	144	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233415.1	s__RF16 sp905233415	77.9411	99	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017439235.1	s__RF16 sp017439235	77.8024	92	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233255.1	s__RF16 sp905233255	77.6099	122	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319645.1	s__RF16 sp900319645	77.5984	140	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.68	95.36	0.92	0.85	3	-
GCA_902769535.1	s__RF16 sp902769535	77.557	94	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017417025.1	s__RF16 sp017417025	77.4926	101	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234835.1	s__RF16 sp905234835	77.4445	109	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.79	96.79	0.85	0.85	2	-
GCA_017962005.1	s__RF16 sp017962005	77.3922	84	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234025.1	s__RF16 sp905234025	77.3733	82	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297215.1	s__RF16 sp016297215	77.3369	101	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321005.1	s__RF16 sp900321005	77.273	97	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.51	96.64	0.88	0.83	5	-
GCA_017551025.1	s__RF16 sp017551025	77.1864	115	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784585.1	s__RF16 sp902784585	77.1822	89	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371785.1	s__RF16 sp002371785	77.1213	120	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	97.16	96.55	0.78	0.72	5	-
GCA_017483945.1	s__RF16 sp017483945	77.1122	90	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.89	98.89	0.87	0.87	2	-
GCA_017471175.1	s__RF16 sp017471175	77.0299	78	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.10	96.10	0.74	0.74	2	-
GCA_902799705.1	s__RF16 sp902799705	77.0111	95	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779705.1	s__RF16 sp902779705	76.8568	85	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.39	98.39	0.92	0.92	2	-
GCA_017450685.1	s__RF16 sp017450685	76.7958	72	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	98.15	98.15	0.91	0.91	2	-
GCA_002351925.1	s__RF16 sp002351925	76.7915	108	752	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:39:28,976] [INFO] GTDB search result was written to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/result_gtdb.tsv
[2023-06-05 00:39:28,977] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:39:28,980] [INFO] DFAST_QC result json was written to GCA_902770385.1_Rumen_uncultured_genome_RUG11566_genomic.fna/dqc_result.json
[2023-06-05 00:39:28,980] [INFO] DFAST_QC completed!
[2023-06-05 00:39:28,980] [INFO] Total running time: 0h1m19s