[2024-01-24 13:02:03,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:03,871] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:03,871] [INFO] DQC Reference Directory: /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference
[2024-01-24 13:02:05,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,105] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg0116d6f2-5243-4b1f-90cf-b02a41a02d38/GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna.gz | prodigal -d GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/cds.fna -a GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:16,285] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:16,286] [INFO] Task started: HMMsearch
[2024-01-24 13:02:16,286] [INFO] Running command: hmmsearch --tblout GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/reference_markers.hmm GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:16,516] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:16,517] [INFO] Found 6/6 markers.
[2024-01-24 13:02:16,548] [INFO] Query marker FASTA was written to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:02:16,548] [INFO] Task started: Blastn
[2024-01-24 13:02:16,548] [INFO] Running command: blastn -query GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/reference_markers.fasta -out GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:17,235] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:17,239] [INFO] Selected 23 target genomes.
[2024-01-24 13:02:17,239] [INFO] Target genome list was writen to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:02:17,247] [INFO] Task started: fastANI
[2024-01-24 13:02:17,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg0116d6f2-5243-4b1f-90cf-b02a41a02d38/GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna.gz --refList GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/target_genomes.txt --output GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:31,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:31,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:31,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:31,394] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:31,394] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:31,394] [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
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	100.0	1103	1108	95	conclusive
Cognatishimia maritima	strain=DSM 28223	GCA_900129685.1	870908	870908	type	True	79.6333	445	1108	95	below_threshold
Pelagimonas phthalicica	strain=DSM 26923	GCA_004364805.1	1037362	1037362	type	True	79.5141	216	1108	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	78.1402	247	1108	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.9898	250	1108	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	77.8465	141	1108	95	below_threshold
Shimia thalassica	strain=CECT 7735	GCA_001458215.1	1715693	1715693	type	True	77.8162	178	1108	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	77.6929	226	1108	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	77.6905	220	1108	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	77.6652	229	1108	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.3505	124	1108	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	77.3393	169	1108	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.3386	127	1108	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.3137	190	1108	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.2976	165	1108	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	77.2254	166	1108	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2018	137	1108	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.9449	122	1108	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7158	141	1108	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.4127	91	1108	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.1299	139	1108	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	76.0266	69	1108	95	below_threshold
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	75.8932	73	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:31,396] [INFO] DFAST Taxonomy check result was written to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:02:31,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:31,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:31,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/checkm_data
[2024-01-24 13:02:31,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:31,432] [INFO] Task started: CheckM
[2024-01-24 13:02:31,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/checkm_input GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/checkm_result
[2024-01-24 13:03:05,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:05,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:05,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:05,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:05,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:03:05,712] [INFO] Task started: Blastn
[2024-01-24 13:03:05,712] [INFO] Running command: blastn -query GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg1147c39f-cce5-4f75-8730-b24fb0cf6d4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:06,675] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:06,678] [INFO] Selected 22 target genomes.
[2024-01-24 13:03:06,678] [INFO] Target genome list was writen to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:06,735] [INFO] Task started: fastANI
[2024-01-24 13:03:06,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg0116d6f2-5243-4b1f-90cf-b02a41a02d38/GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna.gz --refList GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:20,616] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:20,632] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:20,633] [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_001458335.1	s__Cognatishimia activa	100.0	1103	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_900129685.1	s__Cognatishimia maritima	79.6563	443	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364805.1	s__Pelagimonas phthalicica	79.5141	216	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pelagimonas	95.0	97.63	95.26	0.94	0.87	3	-
GCA_013215215.1	s__Cognatishimia sp013215215	78.7136	290	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017798205.1	s__Cognatishimia activa_A	78.3585	331	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458175.1	s__Shimia marina	78.1402	247	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_017743735.1	s__Shimia sp017743735	78.0748	240	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	95.87	95.63	0.93	0.93	3	-
GCF_001458215.1	s__Shimia thalassica	77.8162	178	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	96.93	96.93	0.94	0.94	2	-
GCF_900114415.1	s__Shimia haliotis	77.6905	220	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458415.1	s__Epibacterium multivorans	77.6652	229	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017744095.1	s__Shimia sp017744095	77.6513	233	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001292625.1	s__Shimia sp001292625	77.515	189	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	77.4693	175	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001258055.1	s__Phaeobacter italicus	77.409	199	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.00	98.06	0.96	0.92	7	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.3505	124	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_900172225.1	s__Ruegeria_E litorea	77.3327	188	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900537125.1	s__Shimia sp900537125	77.3085	227	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900143615.1	s__Shimia sp900143615	77.2496	185	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000671395.1	s__Actibacterium atlanticum	77.2254	166	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	77.0556	173	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCA_018223085.1	s__Shimia sp018223085	77.0154	160	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001679925.1	s__Leisingera sp001679925	76.9776	158	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:20,634] [INFO] GTDB search result was written to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:20,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:20,639] [INFO] DFAST_QC result json was written to GCF_001458335.1_Thalassobius_sp._CECT5113_Velvet_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:03:20,639] [INFO] DFAST_QC completed!
[2024-01-24 13:03:20,640] [INFO] Total running time: 0h1m17s