[2023-06-30 02:23:31,410] [INFO] DFAST_QC pipeline started.
[2023-06-30 02:23:31,412] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 02:23:31,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference
[2023-06-30 02:23:32,636] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 02:23:32,637] [INFO] Task started: Prodigal
[2023-06-30 02:23:32,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg8edf2536-cb8b-40fe-8e25-11ddf0b71f7b/GCA_016708585.1_ASM1670858v1_genomic.fna.gz | prodigal -d GCA_016708585.1_ASM1670858v1_genomic.fna/cds.fna -a GCA_016708585.1_ASM1670858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 02:23:43,744] [INFO] Task succeeded: Prodigal
[2023-06-30 02:23:43,744] [INFO] Task started: HMMsearch
[2023-06-30 02:23:43,744] [INFO] Running command: hmmsearch --tblout GCA_016708585.1_ASM1670858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/reference_markers.hmm GCA_016708585.1_ASM1670858v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 02:23:44,003] [INFO] Task succeeded: HMMsearch
[2023-06-30 02:23:44,005] [INFO] Found 6/6 markers.
[2023-06-30 02:23:44,041] [INFO] Query marker FASTA was written to GCA_016708585.1_ASM1670858v1_genomic.fna/markers.fasta
[2023-06-30 02:23:44,041] [INFO] Task started: Blastn
[2023-06-30 02:23:44,041] [INFO] Running command: blastn -query GCA_016708585.1_ASM1670858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/reference_markers.fasta -out GCA_016708585.1_ASM1670858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:23:45,089] [INFO] Task succeeded: Blastn
[2023-06-30 02:23:45,094] [INFO] Selected 24 target genomes.
[2023-06-30 02:23:45,094] [INFO] Target genome list was writen to GCA_016708585.1_ASM1670858v1_genomic.fna/target_genomes.txt
[2023-06-30 02:23:45,096] [INFO] Task started: fastANI
[2023-06-30 02:23:45,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg8edf2536-cb8b-40fe-8e25-11ddf0b71f7b/GCA_016708585.1_ASM1670858v1_genomic.fna.gz --refList GCA_016708585.1_ASM1670858v1_genomic.fna/target_genomes.txt --output GCA_016708585.1_ASM1670858v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 02:24:03,605] [INFO] Task succeeded: fastANI
[2023-06-30 02:24:03,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 02:24:03,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 02:24:03,629] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 02:24:03,630] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 02:24:03,630] [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
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	81.1409	513	1211	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	81.0644	511	1211	95	below_threshold
Sterolibacterium denitrificans	strain=DSM 13999	GCA_001586935.1	157592	157592	type	True	79.4053	114	1211	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	79.1768	393	1211	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	79.0326	412	1211	95	below_threshold
Thauera aminoaromatica	strain=S2	GCA_000310185.1	164330	164330	type	True	78.9755	397	1211	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	78.9597	348	1211	95	below_threshold
Georgfuchsia toluolica	strain=G5G6	GCA_907163265.1	424218	424218	type	True	78.9514	302	1211	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	78.8987	358	1211	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	78.8105	362	1211	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_902813185.1	311182	311182	type	True	78.7909	331	1211	95	below_threshold
Denitratisoma oestradiolicum	strain=DSM 16959	GCA_007844305.1	311182	311182	type	True	78.79	338	1211	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.6283	389	1211	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	78.4554	361	1211	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	78.3355	374	1211	95	below_threshold
Aromatoleum buckelii	strain=U120	GCA_012910785.2	200254	200254	type	True	78.229	316	1211	95	below_threshold
Aromatoleum anaerobium	strain=LuFRes1	GCA_012910705.2	182180	182180	type	True	78.147	352	1211	95	below_threshold
Nitrogeniibacter mangrovi	strain=M9-3-2	GCA_010983895.1	2016596	2016596	type	True	77.8778	331	1211	95	below_threshold
Noviherbaspirillum galbum	strain=17J57-3	GCA_010974945.1	2709383	2709383	type	True	77.6031	264	1211	95	below_threshold
Duganella callida	strain=DN04	GCA_004614165.1	2561932	2561932	type	True	77.081	293	1211	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	77.0525	296	1211	95	below_threshold
Duganella lactea	strain=FT50W	GCA_009857505.1	2692173	2692173	type	True	77.0043	260	1211	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	76.9421	263	1211	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	76.715	282	1211	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 02:24:03,632] [INFO] DFAST Taxonomy check result was written to GCA_016708585.1_ASM1670858v1_genomic.fna/tc_result.tsv
[2023-06-30 02:24:03,633] [INFO] ===== Taxonomy check completed =====
[2023-06-30 02:24:03,633] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 02:24:03,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/checkm_data
[2023-06-30 02:24:03,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 02:24:03,677] [INFO] Task started: CheckM
[2023-06-30 02:24:03,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708585.1_ASM1670858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708585.1_ASM1670858v1_genomic.fna/checkm_input GCA_016708585.1_ASM1670858v1_genomic.fna/checkm_result
[2023-06-30 02:24:41,298] [INFO] Task succeeded: CheckM
[2023-06-30 02:24:41,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 02:24:41,325] [INFO] ===== Completeness check finished =====
[2023-06-30 02:24:41,325] [INFO] ===== Start GTDB Search =====
[2023-06-30 02:24:41,325] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708585.1_ASM1670858v1_genomic.fna/markers.fasta)
[2023-06-30 02:24:41,326] [INFO] Task started: Blastn
[2023-06-30 02:24:41,326] [INFO] Running command: blastn -query GCA_016708585.1_ASM1670858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f05ec6-a8c5-4354-b6b7-ac8b5b8cbf5f/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708585.1_ASM1670858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 02:24:43,436] [INFO] Task succeeded: Blastn
[2023-06-30 02:24:43,441] [INFO] Selected 12 target genomes.
[2023-06-30 02:24:43,441] [INFO] Target genome list was writen to GCA_016708585.1_ASM1670858v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 02:24:43,443] [INFO] Task started: fastANI
[2023-06-30 02:24:43,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg8edf2536-cb8b-40fe-8e25-11ddf0b71f7b/GCA_016708585.1_ASM1670858v1_genomic.fna.gz --refList GCA_016708585.1_ASM1670858v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708585.1_ASM1670858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 02:24:53,728] [INFO] Task succeeded: fastANI
[2023-06-30 02:24:53,744] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 02:24:53,745] [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_016708585.1	s__Sulfuritalea sp016708585	100.0	1210	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903932755.1	s__Sulfuritalea sp903932755	86.5463	425	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	98.78	98.78	0.75	0.75	2	-
GCA_903933395.1	s__Sulfuritalea sp903933395	86.4375	582	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.21	99.21	0.82	0.82	2	-
GCA_017302275.1	s__Sulfuritalea sp017302275	85.8454	793	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012026675.1	s__Sulfuritalea sp012026675	85.5478	662	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716965.1	s__Sulfuritalea sp016716965	85.3438	747	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016192435.1	s__Sulfuritalea sp016192435	85.3106	609	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828635.1	s__Sulfuritalea hydrogenivorans	84.9687	744	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235805.1	s__Sulfuritalea sp016235805	84.6223	621	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215645.1	s__Sulfuritalea sp016215645	83.7247	593	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908065.1	s__Sulfuritalea sp903908065	83.4352	696	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	99.89	99.84	0.95	0.93	5	-
GCA_001828935.1	s__Sulfuritalea sp001828935	83.4171	670	1211	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfuritalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 02:24:53,746] [INFO] GTDB search result was written to GCA_016708585.1_ASM1670858v1_genomic.fna/result_gtdb.tsv
[2023-06-30 02:24:53,747] [INFO] ===== GTDB Search completed =====
[2023-06-30 02:24:53,751] [INFO] DFAST_QC result json was written to GCA_016708585.1_ASM1670858v1_genomic.fna/dqc_result.json
[2023-06-30 02:24:53,752] [INFO] DFAST_QC completed!
[2023-06-30 02:24:53,752] [INFO] Total running time: 0h1m22s