[2024-01-24 12:53:36,084] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,086] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference
[2024-01-24 12:53:37,375] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:37,376] [INFO] Task started: Prodigal
[2024-01-24 12:53:37,376] [INFO] Running command: gunzip -c /var/lib/cwl/stg14f7d5d2-b03b-4371-a76e-e567c0a04b26/GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/cds.fna -a GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:51,497] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:51,497] [INFO] Task started: HMMsearch
[2024-01-24 12:53:51,498] [INFO] Running command: hmmsearch --tblout GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/reference_markers.hmm GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:51,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:51,771] [INFO] Found 6/6 markers.
[2024-01-24 12:53:51,812] [INFO] Query marker FASTA was written to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 12:53:51,813] [INFO] Task started: Blastn
[2024-01-24 12:53:51,813] [INFO] Running command: blastn -query GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/reference_markers.fasta -out GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:52,555] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:52,559] [INFO] Selected 17 target genomes.
[2024-01-24 12:53:52,559] [INFO] Target genome list was writen to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 12:53:52,565] [INFO] Task started: fastANI
[2024-01-24 12:53:52,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f7d5d2-b03b-4371-a76e-e567c0a04b26/GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna.gz --refList GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:06,312] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:06,313] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:06,313] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:06,326] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:06,326] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:06,327] [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
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	100.0	1513	1517	95	conclusive
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	82.1843	890	1517	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	81.895	907	1517	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	81.4123	833	1517	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	81.3245	752	1517	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	81.2573	766	1517	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	80.7934	714	1517	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.6736	728	1517	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	79.1063	534	1517	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.8023	369	1517	95	below_threshold
Tritonibacter aquimaris	strain=SM1969	GCA_009617595.1	2663379	2663379	type	True	77.7682	249	1517	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.4734	330	1517	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.0527	266	1517	95	below_threshold
Salinihabitans flavidus	strain=DSM 27842	GCA_900110425.1	569882	569882	type	True	76.9999	226	1517	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7872	200	1517	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.7109	144	1517	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6515	201	1517	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:06,329] [INFO] DFAST Taxonomy check result was written to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 12:54:06,329] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:06,329] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:06,330] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/checkm_data
[2024-01-24 12:54:06,330] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:06,374] [INFO] Task started: CheckM
[2024-01-24 12:54:06,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/checkm_input GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 12:54:49,973] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:49,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:49,993] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:49,993] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:49,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 12:54:49,994] [INFO] Task started: Blastn
[2024-01-24 12:54:49,995] [INFO] Running command: blastn -query GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg551bc1a3-e404-4034-8796-3b5a7cfc5387/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:51,135] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:51,139] [INFO] Selected 11 target genomes.
[2024-01-24 12:54:51,139] [INFO] Target genome list was writen to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:51,152] [INFO] Task started: fastANI
[2024-01-24 12:54:51,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg14f7d5d2-b03b-4371-a76e-e567c0a04b26/GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna.gz --refList GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:02,155] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:02,171] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:02,171] [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_001458295.1	s__Ruegeria denitrificans	100.0	1513	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013032005.1	s__Ruegeria atlantica_A	87.5014	1119	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	84.0348	1011	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	84.024	1012	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_013032445.1	s__Ruegeria arenilitoris_F	83.6163	1014	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032455.1	s__Ruegeria atlantica_B	83.2374	947	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.37	96.74	0.95	0.90	3	-
GCF_013032095.1	s__Ruegeria atlantica_E	83.1306	1025	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	82.6044	941	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013035315.1	s__Ruegeria arenilitoris_D	82.1291	892	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	95.80	95.80	0.90	0.90	2	-
GCF_013032025.1	s__Ruegeria atlantica_C	81.291	771	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013112245.1	s__Ruegeria sp013112245	81.1899	811	1517	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.18	96.94	0.93	0.89	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:02,173] [INFO] GTDB search result was written to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:02,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:02,177] [INFO] DFAST_QC result json was written to GCF_001458295.1_Ruegeria_sp._CECT5091_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 12:55:02,177] [INFO] DFAST_QC completed!
[2024-01-24 12:55:02,177] [INFO] Total running time: 0h1m26s