[2024-01-24 15:10:23,128] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,130] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference
[2024-01-24 15:10:24,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,690] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgada9de23-e465-450c-b147-f2d4a56f6f65/GCF_007004065.1_ASM700406v1_genomic.fna.gz | prodigal -d GCF_007004065.1_ASM700406v1_genomic.fna/cds.fna -a GCF_007004065.1_ASM700406v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:36,105] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:36,105] [INFO] Task started: HMMsearch
[2024-01-24 15:10:36,106] [INFO] Running command: hmmsearch --tblout GCF_007004065.1_ASM700406v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/reference_markers.hmm GCF_007004065.1_ASM700406v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:36,331] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:36,332] [INFO] Found 6/6 markers.
[2024-01-24 15:10:36,366] [INFO] Query marker FASTA was written to GCF_007004065.1_ASM700406v1_genomic.fna/markers.fasta
[2024-01-24 15:10:36,366] [INFO] Task started: Blastn
[2024-01-24 15:10:36,366] [INFO] Running command: blastn -query GCF_007004065.1_ASM700406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/reference_markers.fasta -out GCF_007004065.1_ASM700406v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:37,237] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:37,241] [INFO] Selected 21 target genomes.
[2024-01-24 15:10:37,241] [INFO] Target genome list was writen to GCF_007004065.1_ASM700406v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:37,249] [INFO] Task started: fastANI
[2024-01-24 15:10:37,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgada9de23-e465-450c-b147-f2d4a56f6f65/GCF_007004065.1_ASM700406v1_genomic.fna.gz --refList GCF_007004065.1_ASM700406v1_genomic.fna/target_genomes.txt --output GCF_007004065.1_ASM700406v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:53,219] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:53,220] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:53,220] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:53,237] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:53,238] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:53,238] [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
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	100.0	1244	1250	95	conclusive
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.0515	301	1250	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.0267	306	1250	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.9969	357	1250	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	77.9936	327	1250	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9222	290	1250	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	77.6083	230	1250	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.5194	284	1250	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.4826	274	1250	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.4386	247	1250	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.3704	227	1250	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	77.3476	247	1250	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.3062	225	1250	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.3004	227	1250	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.299	257	1250	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.2824	252	1250	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.2601	257	1250	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.2529	226	1250	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.0146	192	1250	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.9282	214	1250	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	76.8686	167	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:53,240] [INFO] DFAST Taxonomy check result was written to GCF_007004065.1_ASM700406v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:53,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:53,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:53,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/checkm_data
[2024-01-24 15:10:53,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:53,282] [INFO] Task started: CheckM
[2024-01-24 15:10:53,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004065.1_ASM700406v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004065.1_ASM700406v1_genomic.fna/checkm_input GCF_007004065.1_ASM700406v1_genomic.fna/checkm_result
[2024-01-24 15:11:31,054] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:31,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:31,071] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:31,071] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:31,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004065.1_ASM700406v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:31,072] [INFO] Task started: Blastn
[2024-01-24 15:11:31,072] [INFO] Running command: blastn -query GCF_007004065.1_ASM700406v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d45266b-1c8a-4805-865a-70c4f2ca638e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004065.1_ASM700406v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:32,647] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:32,650] [INFO] Selected 23 target genomes.
[2024-01-24 15:11:32,650] [INFO] Target genome list was writen to GCF_007004065.1_ASM700406v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:32,666] [INFO] Task started: fastANI
[2024-01-24 15:11:32,666] [INFO] Running command: fastANI --query /var/lib/cwl/stgada9de23-e465-450c-b147-f2d4a56f6f65/GCF_007004065.1_ASM700406v1_genomic.fna.gz --refList GCF_007004065.1_ASM700406v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004065.1_ASM700406v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:49,101] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:49,119] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:49,119] [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_007004065.1	s__Palleronia caenipelagi	100.0	1244	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900172315.1	s__Palleronia marisminoris	78.0393	302	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900302445.1	s__Palleronia abyssalis	78.0238	287	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	78.0031	332	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	77.9965	357	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	77.9837	328	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	77.7734	341	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	77.6162	236	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	77.4939	267	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	77.417	252	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.3685	278	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	77.3497	246	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	77.3497	247	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	77.31	265	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900107235.1	s__Citreimonas salinaria	77.2929	225	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.2729	252	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	77.269	281	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	77.2488	238	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	77.2458	225	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCA_016938875.1	s__Rhodovulum sp016938875	77.1231	232	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	76.8689	165	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564655.1	s__Roseinatronobacter sp003564655	76.6829	160	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009922885.1	s__UBA9554 sp009922885	76.6729	97	1250	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA9554	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:49,121] [INFO] GTDB search result was written to GCF_007004065.1_ASM700406v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:49,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:49,128] [INFO] DFAST_QC result json was written to GCF_007004065.1_ASM700406v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:49,128] [INFO] DFAST_QC completed!
[2024-01-24 15:11:49,128] [INFO] Total running time: 0h1m26s