[2023-06-30 15:42:53,277] [INFO] DFAST_QC pipeline started.
[2023-06-30 15:42:53,279] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 15:42:53,279] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference
[2023-06-30 15:42:54,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 15:42:54,598] [INFO] Task started: Prodigal
[2023-06-30 15:42:54,598] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa34465a-7149-403e-82f0-9371ec533dc4/GCA_025458485.1_ASM2545848v1_genomic.fna.gz | prodigal -d GCA_025458485.1_ASM2545848v1_genomic.fna/cds.fna -a GCA_025458485.1_ASM2545848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 15:43:04,338] [INFO] Task succeeded: Prodigal
[2023-06-30 15:43:04,338] [INFO] Task started: HMMsearch
[2023-06-30 15:43:04,338] [INFO] Running command: hmmsearch --tblout GCA_025458485.1_ASM2545848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/reference_markers.hmm GCA_025458485.1_ASM2545848v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 15:43:04,537] [INFO] Task succeeded: HMMsearch
[2023-06-30 15:43:04,538] [INFO] Found 6/6 markers.
[2023-06-30 15:43:04,574] [INFO] Query marker FASTA was written to GCA_025458485.1_ASM2545848v1_genomic.fna/markers.fasta
[2023-06-30 15:43:04,574] [INFO] Task started: Blastn
[2023-06-30 15:43:04,574] [INFO] Running command: blastn -query GCA_025458485.1_ASM2545848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/reference_markers.fasta -out GCA_025458485.1_ASM2545848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:43:05,489] [INFO] Task succeeded: Blastn
[2023-06-30 15:43:05,493] [INFO] Selected 34 target genomes.
[2023-06-30 15:43:05,493] [INFO] Target genome list was writen to GCA_025458485.1_ASM2545848v1_genomic.fna/target_genomes.txt
[2023-06-30 15:43:05,509] [INFO] Task started: fastANI
[2023-06-30 15:43:05,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa34465a-7149-403e-82f0-9371ec533dc4/GCA_025458485.1_ASM2545848v1_genomic.fna.gz --refList GCA_025458485.1_ASM2545848v1_genomic.fna/target_genomes.txt --output GCA_025458485.1_ASM2545848v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 15:43:28,489] [INFO] Task succeeded: fastANI
[2023-06-30 15:43:28,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 15:43:28,489] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 15:43:28,515] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 15:43:28,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 15:43:28,516] [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
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	77.8363	302	1061	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	77.8199	331	1061	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.7455	343	1061	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	77.7192	352	1061	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	77.6924	349	1061	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.6538	317	1061	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	77.6168	350	1061	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5528	343	1061	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.4797	323	1061	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.3997	345	1061	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	77.3971	273	1061	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	77.3946	307	1061	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.3591	351	1061	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	77.3063	282	1061	95	below_threshold
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	77.2738	326	1061	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	77.2579	286	1061	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.2542	295	1061	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.2454	297	1061	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.1482	242	1061	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	77.1463	329	1061	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.1416	330	1061	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	77.1004	255	1061	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	77.0899	323	1061	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.0487	299	1061	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	76.9811	310	1061	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	76.9683	302	1061	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.9611	210	1061	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.9441	240	1061	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	76.856	302	1061	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	76.8557	228	1061	95	below_threshold
Tropicimonas isoalkanivorans	strain=DSM 19548	GCA_900112335.1	441112	441112	type	True	76.8258	203	1061	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	76.7431	255	1061	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.7271	258	1061	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	76.7144	257	1061	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 15:43:28,518] [INFO] DFAST Taxonomy check result was written to GCA_025458485.1_ASM2545848v1_genomic.fna/tc_result.tsv
[2023-06-30 15:43:28,519] [INFO] ===== Taxonomy check completed =====
[2023-06-30 15:43:28,519] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 15:43:28,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/checkm_data
[2023-06-30 15:43:28,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 15:43:28,559] [INFO] Task started: CheckM
[2023-06-30 15:43:28,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025458485.1_ASM2545848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025458485.1_ASM2545848v1_genomic.fna/checkm_input GCA_025458485.1_ASM2545848v1_genomic.fna/checkm_result
[2023-06-30 15:44:03,875] [INFO] Task succeeded: CheckM
[2023-06-30 15:44:03,876] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 15:44:03,896] [INFO] ===== Completeness check finished =====
[2023-06-30 15:44:03,896] [INFO] ===== Start GTDB Search =====
[2023-06-30 15:44:03,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025458485.1_ASM2545848v1_genomic.fna/markers.fasta)
[2023-06-30 15:44:03,896] [INFO] Task started: Blastn
[2023-06-30 15:44:03,897] [INFO] Running command: blastn -query GCA_025458485.1_ASM2545848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf959c98-a7e3-42b3-91f5-1d384e7cdfa0/dqc_reference/reference_markers_gtdb.fasta -out GCA_025458485.1_ASM2545848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 15:44:05,583] [INFO] Task succeeded: Blastn
[2023-06-30 15:44:05,587] [INFO] Selected 30 target genomes.
[2023-06-30 15:44:05,587] [INFO] Target genome list was writen to GCA_025458485.1_ASM2545848v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 15:44:05,597] [INFO] Task started: fastANI
[2023-06-30 15:44:05,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa34465a-7149-403e-82f0-9371ec533dc4/GCA_025458485.1_ASM2545848v1_genomic.fna.gz --refList GCA_025458485.1_ASM2545848v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025458485.1_ASM2545848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 15:44:24,940] [INFO] Task succeeded: fastANI
[2023-06-30 15:44:24,967] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 15:44:24,967] [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
GCA_002291955.1	s__UBA996 sp002291955	87.9302	619	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA996	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	77.9698	375	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	77.8397	329	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	77.8275	354	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	77.826	303	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	77.7551	342	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	77.6945	289	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	77.6811	351	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	77.6312	324	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	77.6174	234	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	77.5888	341	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401465.1	s__Aestuariivita sp018401465	77.5328	327	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	77.4141	292	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	77.3919	346	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	77.3885	242	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841115.1	s__Albidovulum sp002841115	77.3798	316	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	77.3611	257	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622145.1	s__Paracoccus yeei	77.3484	299	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCA_003605175.1	s__IMCC34051 sp003605175	77.3247	294	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522155.1	s__Paracoccus luteus	77.298	323	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.2872	316	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763805.1	s__Paracoccus sphaerophysae	77.2293	289	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	77.1944	313	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_900108275.1	s__Jhaorihella thermophila	77.1762	281	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	77.1547	327	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.1456	281	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.1154	350	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_016446475.1	s__Paracoccus binzhouensis	77.0978	322	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	77.0435	248	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390845.1	s__Tropicimonas sp003390845	76.8488	293	1061	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 15:44:24,969] [INFO] GTDB search result was written to GCA_025458485.1_ASM2545848v1_genomic.fna/result_gtdb.tsv
[2023-06-30 15:44:24,970] [INFO] ===== GTDB Search completed =====
[2023-06-30 15:44:24,976] [INFO] DFAST_QC result json was written to GCA_025458485.1_ASM2545848v1_genomic.fna/dqc_result.json
[2023-06-30 15:44:24,976] [INFO] DFAST_QC completed!
[2023-06-30 15:44:24,976] [INFO] Total running time: 0h1m32s