[2024-01-24 13:08:58,404] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:08:58,405] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:08:58,405] [INFO] DQC Reference Directory: /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference
[2024-01-24 13:08:59,676] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:08:59,677] [INFO] Task started: Prodigal
[2024-01-24 13:08:59,677] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8eb224a-1793-4afd-b7a4-ea5d78fac8f3/GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:12,906] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:12,906] [INFO] Task started: HMMsearch
[2024-01-24 13:09:12,907] [INFO] Running command: hmmsearch --tblout GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/reference_markers.hmm GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:13,166] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:13,167] [INFO] Found 6/6 markers.
[2024-01-24 13:09:13,204] [INFO] Query marker FASTA was written to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 13:09:13,204] [INFO] Task started: Blastn
[2024-01-24 13:09:13,204] [INFO] Running command: blastn -query GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/reference_markers.fasta -out GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:14,076] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:14,079] [INFO] Selected 17 target genomes.
[2024-01-24 13:09:14,079] [INFO] Target genome list was writen to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 13:09:14,099] [INFO] Task started: fastANI
[2024-01-24 13:09:14,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8eb224a-1793-4afd-b7a4-ea5d78fac8f3/GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna.gz --refList GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:27,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:27,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:27,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:27,726] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:27,726] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:27,726] [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
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	100.0	1304	1308	95	conclusive
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	92.8091	1045	1308	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	88.319	967	1308	95	below_threshold
Roseovarius azorensis	strain=DSM 100674	GCA_900109455.1	1287727	1287727	type	True	79.8518	668	1308	95	below_threshold
Roseovarius tolerans	strain=DSM 11457	GCA_900109855.1	74031	74031	type	True	79.7891	703	1308	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	79.6267	552	1308	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	79.045	551	1308	95	below_threshold
Roseovarius nubinhibens	strain=ISM	GCA_000152625.1	314263	314263	type	True	79.016	502	1308	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.2407	450	1308	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.2125	456	1308	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.1948	461	1308	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.6006	298	1308	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.547	263	1308	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5157	302	1308	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.2704	274	1308	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.1962	235	1308	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.7548	187	1308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:27,728] [INFO] DFAST Taxonomy check result was written to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 13:09:27,728] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:27,729] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:27,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/checkm_data
[2024-01-24 13:09:27,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:27,772] [INFO] Task started: CheckM
[2024-01-24 13:09:27,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/checkm_input GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 13:10:10,040] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:10,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:10,062] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:10,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:10,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 13:10:10,063] [INFO] Task started: Blastn
[2024-01-24 13:10:10,064] [INFO] Running command: blastn -query GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgce34d402-fc17-44bd-b69c-507607e9dd2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:11,730] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:11,733] [INFO] Selected 14 target genomes.
[2024-01-24 13:10:11,733] [INFO] Target genome list was writen to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:11,763] [INFO] Task started: fastANI
[2024-01-24 13:10:11,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8eb224a-1793-4afd-b7a4-ea5d78fac8f3/GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna.gz --refList GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:23,465] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:23,482] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:23,483] [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_900172365.1	s__Roseovarius gaetbuli	100.0	1304	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142625.1	s__Roseovarius marisflavi	92.8018	1046	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	88.3331	966	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066915.1	s__Roseovarius sp018066915	79.9258	621	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.88	99.88	0.93	0.93	2	-
GCF_900109455.1	s__Roseovarius azorensis	79.8516	668	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172295.1	s__Roseovarius litorisediminis	79.6574	550	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002080415.1	s__Roseovarius mucosus_A	79.4917	658	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.86	96.11	0.91	0.79	6	-
GCF_900142665.1	s__Roseovarius pacificus	79.0816	551	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	97.52	95.05	0.91	0.82	3	-
GCF_000152625.1	s__Roseovarius nubinhibens	79.0196	501	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_003072125.1	s__Roseovarius sediminicola	78.2474	450	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.2043	457	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	78.1869	462	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_900156535.1	s__Roseovarius nanhaiticus	78.0679	412	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000429365.1	s__Pseudodonghicola xiamenensis	77.7247	332	1308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudodonghicola	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:23,484] [INFO] GTDB search result was written to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:23,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:23,489] [INFO] DFAST_QC result json was written to GCF_900172365.1_R.gaetbulli_CECT8370_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 13:10:23,489] [INFO] DFAST_QC completed!
[2024-01-24 13:10:23,489] [INFO] Total running time: 0h1m25s