[2023-06-28 02:42:32,051] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:42:32,053] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:42:32,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference
[2023-06-28 02:42:33,370] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:42:33,370] [INFO] Task started: Prodigal
[2023-06-28 02:42:33,371] [INFO] Running command: gunzip -c /var/lib/cwl/stga209e460-6bc8-4b87-a02a-6770aaf6419f/GCA_017412145.1_ASM1741214v1_genomic.fna.gz | prodigal -d GCA_017412145.1_ASM1741214v1_genomic.fna/cds.fna -a GCA_017412145.1_ASM1741214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:42:47,607] [INFO] Task succeeded: Prodigal
[2023-06-28 02:42:47,607] [INFO] Task started: HMMsearch
[2023-06-28 02:42:47,607] [INFO] Running command: hmmsearch --tblout GCA_017412145.1_ASM1741214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/reference_markers.hmm GCA_017412145.1_ASM1741214v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:42:47,870] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:42:47,872] [INFO] Found 6/6 markers.
[2023-06-28 02:42:47,900] [INFO] Query marker FASTA was written to GCA_017412145.1_ASM1741214v1_genomic.fna/markers.fasta
[2023-06-28 02:42:47,900] [INFO] Task started: Blastn
[2023-06-28 02:42:47,900] [INFO] Running command: blastn -query GCA_017412145.1_ASM1741214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/reference_markers.fasta -out GCA_017412145.1_ASM1741214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:42:48,551] [INFO] Task succeeded: Blastn
[2023-06-28 02:42:48,556] [INFO] Selected 25 target genomes.
[2023-06-28 02:42:48,557] [INFO] Target genome list was writen to GCA_017412145.1_ASM1741214v1_genomic.fna/target_genomes.txt
[2023-06-28 02:42:48,558] [INFO] Task started: fastANI
[2023-06-28 02:42:48,558] [INFO] Running command: fastANI --query /var/lib/cwl/stga209e460-6bc8-4b87-a02a-6770aaf6419f/GCA_017412145.1_ASM1741214v1_genomic.fna.gz --refList GCA_017412145.1_ASM1741214v1_genomic.fna/target_genomes.txt --output GCA_017412145.1_ASM1741214v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:43:01,220] [INFO] Task succeeded: fastANI
[2023-06-28 02:43:01,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:43:01,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:43:01,233] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:43:01,234] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:43:01,234] [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 dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.5501	102	758	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.5307	103	758	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.4954	99	758	95	below_threshold
Prevotella baroniae	strain=JCM 13447	GCA_000613565.1	305719	305719	type	True	76.4792	89	758	95	below_threshold
Prevotella baroniae	strain=DSM 16972	GCA_000426585.1	305719	305719	type	True	76.4715	91	758	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.4508	60	758	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	76.3126	89	758	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	76.2834	59	758	95	below_threshold
Prevotella loescheii	strain=DSM 19665	GCA_000378085.1	840	840	type	True	76.2726	50	758	95	below_threshold
Prevotella lacticifex	strain=R5019	GCA_019973375.1	2854755	2854755	type	True	76.2694	54	758	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	76.2551	59	758	95	below_threshold
Prevotella loescheii	strain=JCM 12249	GCA_000613485.1	840	840	type	True	76.2195	52	758	95	below_threshold
Prevotella loescheii	strain=ATCC 15930	GCA_000698925.1	840	840	type	True	76.2015	52	758	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.8824	63	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:43:01,236] [INFO] DFAST Taxonomy check result was written to GCA_017412145.1_ASM1741214v1_genomic.fna/tc_result.tsv
[2023-06-28 02:43:01,236] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:43:01,237] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:43:01,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/checkm_data
[2023-06-28 02:43:01,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:43:01,268] [INFO] Task started: CheckM
[2023-06-28 02:43:01,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017412145.1_ASM1741214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017412145.1_ASM1741214v1_genomic.fna/checkm_input GCA_017412145.1_ASM1741214v1_genomic.fna/checkm_result
[2023-06-28 02:43:44,583] [INFO] Task succeeded: CheckM
[2023-06-28 02:43:44,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.31%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:43:44,606] [INFO] ===== Completeness check finished =====
[2023-06-28 02:43:44,606] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:43:44,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017412145.1_ASM1741214v1_genomic.fna/markers.fasta)
[2023-06-28 02:43:44,607] [INFO] Task started: Blastn
[2023-06-28 02:43:44,607] [INFO] Running command: blastn -query GCA_017412145.1_ASM1741214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43727d3d-4b53-4d4a-bf8c-98296b144082/dqc_reference/reference_markers_gtdb.fasta -out GCA_017412145.1_ASM1741214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:43:45,468] [INFO] Task succeeded: Blastn
[2023-06-28 02:43:45,473] [INFO] Selected 15 target genomes.
[2023-06-28 02:43:45,473] [INFO] Target genome list was writen to GCA_017412145.1_ASM1741214v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:43:45,480] [INFO] Task started: fastANI
[2023-06-28 02:43:45,481] [INFO] Running command: fastANI --query /var/lib/cwl/stga209e460-6bc8-4b87-a02a-6770aaf6419f/GCA_017412145.1_ASM1741214v1_genomic.fna.gz --refList GCA_017412145.1_ASM1741214v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017412145.1_ASM1741214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:43:53,775] [INFO] Task succeeded: fastANI
[2023-06-28 02:43:53,792] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 02:43:53,793] [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_902776665.1	s__Prevotella sp902776665	95.1303	609	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.95	95.21	0.85	0.80	6	conclusive
GCA_017538195.1	s__Prevotella sp017538195	87.424	502	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372575.1	s__Prevotella sp002372575	84.6957	385	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.54	96.38	0.83	0.80	3	-
GCA_017483785.1	s__Prevotella sp017483785	82.9093	366	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902781315.1	s__Prevotella sp902781315	78.7289	295	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.55	96.55	0.79	0.79	2	-
GCA_017557185.1	s__Prevotella sp017557185	78.2514	239	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316285.1	s__Prevotella sp900316285	78.0156	257	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.02	95.37	0.87	0.79	21	-
GCA_902774815.1	s__Prevotella sp902774815	77.621	214	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557405.1	s__Prevotella sp017557405	77.445	146	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769705.1	s__Prevotella sp902769705	77.4168	170	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	96.53	0.84	0.80	3	-
GCA_902776685.1	s__Prevotella sp902776685	77.4044	132	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233425.1	s__Prevotella sp905233425	77.2407	122	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800435.1	s__Prevotella sp902800435	77.1642	126	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.98	95.98	0.77	0.77	2	-
GCA_017395215.1	s__Prevotella sp017395215	77.022	127	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017428805.1	s__Prevotella sp017428805	76.7368	103	758	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:43:53,795] [INFO] GTDB search result was written to GCA_017412145.1_ASM1741214v1_genomic.fna/result_gtdb.tsv
[2023-06-28 02:43:53,796] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:43:53,802] [INFO] DFAST_QC result json was written to GCA_017412145.1_ASM1741214v1_genomic.fna/dqc_result.json
[2023-06-28 02:43:53,802] [INFO] DFAST_QC completed!
[2023-06-28 02:43:53,802] [INFO] Total running time: 0h1m22s