[2024-01-24 14:14:47,304] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:47,306] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:47,306] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference
[2024-01-24 14:14:49,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,428] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,429] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5c63fe3-8363-4b10-9903-012a320cd301/GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/cds.fna -a GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:02,780] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:02,781] [INFO] Task started: HMMsearch
[2024-01-24 14:15:02,781] [INFO] Running command: hmmsearch --tblout GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/reference_markers.hmm GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:03,106] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:03,108] [INFO] Found 6/6 markers.
[2024-01-24 14:15:03,151] [INFO] Query marker FASTA was written to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 14:15:03,151] [INFO] Task started: Blastn
[2024-01-24 14:15:03,152] [INFO] Running command: blastn -query GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/reference_markers.fasta -out GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:04,051] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:04,054] [INFO] Selected 20 target genomes.
[2024-01-24 14:15:04,055] [INFO] Target genome list was writen to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 14:15:04,064] [INFO] Task started: fastANI
[2024-01-24 14:15:04,065] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c63fe3-8363-4b10-9903-012a320cd301/GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna.gz --refList GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:17,524] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:17,525] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:17,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:17,540] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:17,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:17,540] [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
Roseibaca ekhonensis	strain=CECT 7235	GCA_900499075.1	254356	254356	type	True	100.0	1201	1203	95	conclusive
Roseinatronobacter thiooxidans	strain=ALG1	GCA_001870675.1	121821	121821	type	True	78.8782	453	1203	95	below_threshold
Roseinatronobacter thiooxidans	strain=DSM 13087	GCA_003254005.1	121821	121821	type	True	78.8386	455	1203	95	below_threshold
Roseicitreum antarcticum	strain=CGMCC 1.8894	GCA_900107025.1	564137	564137	type	True	78.8063	330	1203	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	78.7943	343	1203	95	below_threshold
Rhodobaca barguzinensis	strain=alga05	GCA_001870665.2	441209	441209	suspected-type	True	78.3237	418	1203	95	below_threshold
Rhodobaca bogoriensis	strain=LBB1	GCA_014197665.1	119542	119542	suspected-type	True	78.2959	418	1203	95	below_threshold
Rhodobaca barguzinensis	strain=DSM 19920	GCA_004365885.1	441209	441209	suspected-type	True	78.2443	409	1203	95	below_threshold
Rhodobaca bogoriensis	strain=DSM 18756	GCA_004366635.1	119542	119542	suspected-type	True	78.225	414	1203	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.1342	364	1203	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.777	254	1203	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	77.6707	295	1203	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.6177	282	1203	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.5661	225	1203	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5402	252	1203	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.4252	274	1203	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.4144	275	1203	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.9303	222	1203	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.9159	183	1203	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	76.5919	183	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:17,542] [INFO] DFAST Taxonomy check result was written to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 14:15:17,543] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:17,543] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:17,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/checkm_data
[2024-01-24 14:15:17,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:17,582] [INFO] Task started: CheckM
[2024-01-24 14:15:17,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/checkm_input GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 14:15:56,574] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:56,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:56,594] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:56,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:56,595] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 14:15:56,595] [INFO] Task started: Blastn
[2024-01-24 14:15:56,596] [INFO] Running command: blastn -query GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd83bd1b-fb06-4b03-b723-562ff696f186/dqc_reference/reference_markers_gtdb.fasta -out GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:58,157] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:58,161] [INFO] Selected 13 target genomes.
[2024-01-24 14:15:58,161] [INFO] Target genome list was writen to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:58,192] [INFO] Task started: fastANI
[2024-01-24 14:15:58,192] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5c63fe3-8363-4b10-9903-012a320cd301/GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna.gz --refList GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:06,779] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:06,794] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:06,794] [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
GCF_900499075.1	s__Roseinatronobacter ekhonensis	100.0	1201	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908405.1	s__Roseinatronobacter sp009908405	83.499	557	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001517585.1	s__Roseinatronobacter calidilacus	83.4199	745	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016937725.1	s__Roseinatronobacter sp016937725	82.5706	547	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001884735.1	s__Roseinatronobacter thiooxidans_A	78.9791	502	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001870675.1	s__Roseinatronobacter thiooxidans	78.8774	453	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	97.65	95.32	0.95	0.92	3	-
GCA_003561595.1	s__Roseinatronobacter sp003561595	78.7541	408	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	98.99	98.90	0.87	0.78	5	-
GCA_007118295.1	s__Roseinatronobacter sp007118295	78.6907	417	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.27	99.27	0.83	0.83	2	-
GCA_007118445.1	s__Roseinatronobacter sp007118445	78.3603	374	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	99.03	98.90	0.77	0.72	3	-
GCF_004366635.1	s__Roseinatronobacter bogoriensis	78.2504	414	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	100.00	99.99	0.99	0.99	4	-
GCA_007116445.1	s__Roseinatronobacter sp007116445	77.9308	241	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007117255.1	s__Roseinatronobacter sp007117255	77.9255	266	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565055.1	s__Roseinatronobacter sp003565055	77.7152	305	1203	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:06,796] [INFO] GTDB search result was written to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:06,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:06,801] [INFO] DFAST_QC result json was written to GCF_900499075.1_R.ekhonensisCECT7235_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 14:16:06,801] [INFO] DFAST_QC completed!
[2024-01-24 14:16:06,801] [INFO] Total running time: 0h1m19s