[2023-06-30 22:12:05,630] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:12:05,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:12:05,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference
[2023-06-30 22:12:08,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:12:08,195] [INFO] Task started: Prodigal
[2023-06-30 22:12:08,195] [INFO] Running command: gunzip -c /var/lib/cwl/stgaccc8077-52ec-402c-88a8-414c2ebf3694/GCA_007131465.1_ASM713146v1_genomic.fna.gz | prodigal -d GCA_007131465.1_ASM713146v1_genomic.fna/cds.fna -a GCA_007131465.1_ASM713146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:12:15,941] [INFO] Task succeeded: Prodigal
[2023-06-30 22:12:15,942] [INFO] Task started: HMMsearch
[2023-06-30 22:12:15,942] [INFO] Running command: hmmsearch --tblout GCA_007131465.1_ASM713146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/reference_markers.hmm GCA_007131465.1_ASM713146v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:12:16,165] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:12:16,167] [INFO] Found 6/6 markers.
[2023-06-30 22:12:16,201] [INFO] Query marker FASTA was written to GCA_007131465.1_ASM713146v1_genomic.fna/markers.fasta
[2023-06-30 22:12:16,201] [INFO] Task started: Blastn
[2023-06-30 22:12:16,202] [INFO] Running command: blastn -query GCA_007131465.1_ASM713146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/reference_markers.fasta -out GCA_007131465.1_ASM713146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:12:17,059] [INFO] Task succeeded: Blastn
[2023-06-30 22:12:17,064] [INFO] Selected 15 target genomes.
[2023-06-30 22:12:17,065] [INFO] Target genome list was writen to GCA_007131465.1_ASM713146v1_genomic.fna/target_genomes.txt
[2023-06-30 22:12:17,106] [INFO] Task started: fastANI
[2023-06-30 22:12:17,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccc8077-52ec-402c-88a8-414c2ebf3694/GCA_007131465.1_ASM713146v1_genomic.fna.gz --refList GCA_007131465.1_ASM713146v1_genomic.fna/target_genomes.txt --output GCA_007131465.1_ASM713146v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:12:26,592] [INFO] Task succeeded: fastANI
[2023-06-30 22:12:26,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:12:26,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:12:26,605] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:12:26,605] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:12:26,606] [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
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	79.9577	378	718	95	below_threshold
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	79.9257	375	718	95	below_threshold
Roseinatronobacter monicus	strain=DSM 18423	GCA_006716865.1	393481	393481	type	True	79.3992	374	718	95	below_threshold
Rhodobaca bogoriensis	strain=LBB1	GCA_014197665.1	119542	119542	suspected-type	True	79.2377	353	718	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	79.1997	352	718	95	below_threshold
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	79.1968	353	718	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	79.1779	354	718	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.4031	279	718	95	below_threshold
Roseibaca ekhonensis	strain=CECT 7235	GCA_900499075.1	254356	254356	type	True	78.0645	281	718	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.4092	199	718	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.9501	167	718	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.9501	167	718	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.8809	182	718	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	76.6102	168	718	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.2465	139	718	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:12:26,608] [INFO] DFAST Taxonomy check result was written to GCA_007131465.1_ASM713146v1_genomic.fna/tc_result.tsv
[2023-06-30 22:12:26,609] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:12:26,609] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:12:26,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/checkm_data
[2023-06-30 22:12:26,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:12:26,646] [INFO] Task started: CheckM
[2023-06-30 22:12:26,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007131465.1_ASM713146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007131465.1_ASM713146v1_genomic.fna/checkm_input GCA_007131465.1_ASM713146v1_genomic.fna/checkm_result
[2023-06-30 22:12:54,582] [INFO] Task succeeded: CheckM
[2023-06-30 22:12:54,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 22:12:54,606] [INFO] ===== Completeness check finished =====
[2023-06-30 22:12:54,607] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:12:54,607] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007131465.1_ASM713146v1_genomic.fna/markers.fasta)
[2023-06-30 22:12:54,608] [INFO] Task started: Blastn
[2023-06-30 22:12:54,608] [INFO] Running command: blastn -query GCA_007131465.1_ASM713146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234f41ec-c012-43ef-9431-85a14d50b844/dqc_reference/reference_markers_gtdb.fasta -out GCA_007131465.1_ASM713146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:12:56,193] [INFO] Task succeeded: Blastn
[2023-06-30 22:12:56,197] [INFO] Selected 16 target genomes.
[2023-06-30 22:12:56,198] [INFO] Target genome list was writen to GCA_007131465.1_ASM713146v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:12:56,212] [INFO] Task started: fastANI
[2023-06-30 22:12:56,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgaccc8077-52ec-402c-88a8-414c2ebf3694/GCA_007131465.1_ASM713146v1_genomic.fna.gz --refList GCA_007131465.1_ASM713146v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007131465.1_ASM713146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:13:05,091] [INFO] Task succeeded: fastANI
[2023-06-30 22:13:05,121] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:13:05,122] [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_007131465.1	s__Roseinatronobacter sp007131465	100.0	709	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	80.5405	382	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003567315.1	s__Roseinatronobacter sp003567315	80.2694	357	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	80.1651	364	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	80.1421	343	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_007128135.1	s__Roseinatronobacter sp007128135	79.9806	352	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.53	99.53	0.93	0.93	2	-
GCA_007118445.1	s__Roseinatronobacter sp007118445	79.9247	320	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.03	98.90	0.77	0.72	3	-
GCA_007692585.1	s__Roseinatronobacter sp007692585	79.5315	330	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134865.1	s__Roseinatronobacter sp007134865	79.3748	316	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.54	99.18	0.88	0.81	5	-
GCA_007123015.1	s__Roseinatronobacter sp007123015	79.1983	268	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.58	99.58	0.86	0.86	2	-
GCA_007125005.1	s__Roseinatronobacter sp007125005	79.1955	288	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.77	99.76	0.94	0.93	3	-
GCA_007694945.1	s__Roseinatronobacter sp007694945	79.0844	331	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007134805.1	s__Roseinatronobacter sp007134805	78.9277	250	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.08	99.08	0.63	0.63	2	-
GCA_007116445.1	s__Roseinatronobacter sp007116445	78.5587	231	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937725.1	s__Roseinatronobacter sp016937725	78.2171	232	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900499075.1	s__Roseinatronobacter ekhonensis	78.0821	281	718	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:13:05,125] [INFO] GTDB search result was written to GCA_007131465.1_ASM713146v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:13:05,125] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:13:05,131] [INFO] DFAST_QC result json was written to GCA_007131465.1_ASM713146v1_genomic.fna/dqc_result.json
[2023-06-30 22:13:05,131] [INFO] DFAST_QC completed!
[2023-06-30 22:13:05,131] [INFO] Total running time: 0h0m60s