[2024-01-24 10:47:24,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:24,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:24,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference
[2024-01-24 10:47:26,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,506] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,506] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2aa8e97-63f4-4e2a-bfd2-676b36277c5c/GCF_003970735.1_ASM397073v1_genomic.fna.gz | prodigal -d GCF_003970735.1_ASM397073v1_genomic.fna/cds.fna -a GCF_003970735.1_ASM397073v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:38,769] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:38,770] [INFO] Task started: HMMsearch
[2024-01-24 10:47:38,770] [INFO] Running command: hmmsearch --tblout GCF_003970735.1_ASM397073v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/reference_markers.hmm GCF_003970735.1_ASM397073v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:39,052] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:39,054] [INFO] Found 6/6 markers.
[2024-01-24 10:47:39,096] [INFO] Query marker FASTA was written to GCF_003970735.1_ASM397073v1_genomic.fna/markers.fasta
[2024-01-24 10:47:39,097] [INFO] Task started: Blastn
[2024-01-24 10:47:39,097] [INFO] Running command: blastn -query GCF_003970735.1_ASM397073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/reference_markers.fasta -out GCF_003970735.1_ASM397073v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:40,115] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:40,119] [INFO] Selected 22 target genomes.
[2024-01-24 10:47:40,120] [INFO] Target genome list was writen to GCF_003970735.1_ASM397073v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:40,128] [INFO] Task started: fastANI
[2024-01-24 10:47:40,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aa8e97-63f4-4e2a-bfd2-676b36277c5c/GCF_003970735.1_ASM397073v1_genomic.fna.gz --refList GCF_003970735.1_ASM397073v1_genomic.fna/target_genomes.txt --output GCF_003970735.1_ASM397073v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:57,021] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:57,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:57,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:57,038] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:57,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:57,039] [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
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	100.0	1450	1450	95	conclusive
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	99.984	1431	1450	95	conclusive
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.8387	481	1450	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.8302	483	1450	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.8031	488	1450	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.6782	468	1450	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.2532	377	1450	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.098	341	1450	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.0851	343	1450	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.0634	397	1450	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	78.0311	357	1450	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	78.0123	365	1450	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.0004	401	1450	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.9571	321	1450	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.9374	371	1450	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.8213	363	1450	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	77.6275	341	1450	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6237	298	1450	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6195	302	1450	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	77.6175	313	1450	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	77.6	304	1450	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.0245	238	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:57,040] [INFO] DFAST Taxonomy check result was written to GCF_003970735.1_ASM397073v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:57,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:57,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:57,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/checkm_data
[2024-01-24 10:47:57,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:57,084] [INFO] Task started: CheckM
[2024-01-24 10:47:57,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003970735.1_ASM397073v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003970735.1_ASM397073v1_genomic.fna/checkm_input GCF_003970735.1_ASM397073v1_genomic.fna/checkm_result
[2024-01-24 10:48:37,667] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:37,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:37,691] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:37,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:37,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003970735.1_ASM397073v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:37,692] [INFO] Task started: Blastn
[2024-01-24 10:48:37,692] [INFO] Running command: blastn -query GCF_003970735.1_ASM397073v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09ed98f5-650b-4df4-9ef2-70de4cd1a52d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003970735.1_ASM397073v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:39,656] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:39,660] [INFO] Selected 25 target genomes.
[2024-01-24 10:48:39,661] [INFO] Target genome list was writen to GCF_003970735.1_ASM397073v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:39,678] [INFO] Task started: fastANI
[2024-01-24 10:48:39,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2aa8e97-63f4-4e2a-bfd2-676b36277c5c/GCF_003970735.1_ASM397073v1_genomic.fna.gz --refList GCF_003970735.1_ASM397073v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003970735.1_ASM397073v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:58,607] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:58,629] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:58,629] [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_003148765.1	s__Silicimonas algicola	99.984	1431	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002869745.1	s__Oceaniglobus roseus	78.9339	507	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.8387	481	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCA_009830125.1	s__GH1-50 sp009830125	78.6918	467	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.6518	464	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.5106	462	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	78.2983	358	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	78.2772	406	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.2683	422	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142295.1	s__Vannielia litorea	78.2492	395	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.1288	442	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.0851	384	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016918935.1	s__MCCB-386 sp016918935	78.0222	364	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MCCB-386	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.0166	398	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	77.9533	335	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_003340565.1	s__HLUCCA09 sp003340565	77.9482	405	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	77.8632	383	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_900112685.1	s__Roseivivax sediminis	77.8376	396	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	77.8304	362	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	77.8217	396	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_002166865.1	s__Roseovarius sp002166865	77.8203	295	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.742	320	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	77.6107	303	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	77.5429	328	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	77.2412	264	1450	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,631] [INFO] GTDB search result was written to GCF_003970735.1_ASM397073v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:58,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:58,636] [INFO] DFAST_QC result json was written to GCF_003970735.1_ASM397073v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:58,636] [INFO] DFAST_QC completed!
[2024-01-24 10:48:58,636] [INFO] Total running time: 0h1m34s