[2023-06-28 20:40:52,058] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:40:52,061] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:40:52,061] [INFO] DQC Reference Directory: /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference
[2023-06-28 20:40:54,146] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:40:54,147] [INFO] Task started: Prodigal
[2023-06-28 20:40:54,147] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e292d0c-8588-48af-836a-0919bbdf988a/GCA_020832515.1_ASM2083251v1_genomic.fna.gz | prodigal -d GCA_020832515.1_ASM2083251v1_genomic.fna/cds.fna -a GCA_020832515.1_ASM2083251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:41:05,265] [INFO] Task succeeded: Prodigal
[2023-06-28 20:41:05,265] [INFO] Task started: HMMsearch
[2023-06-28 20:41:05,265] [INFO] Running command: hmmsearch --tblout GCA_020832515.1_ASM2083251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/reference_markers.hmm GCA_020832515.1_ASM2083251v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:41:05,550] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:41:05,552] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0e292d0c-8588-48af-836a-0919bbdf988a/GCA_020832515.1_ASM2083251v1_genomic.fna.gz]
[2023-06-28 20:41:05,595] [INFO] Query marker FASTA was written to GCA_020832515.1_ASM2083251v1_genomic.fna/markers.fasta
[2023-06-28 20:41:05,595] [INFO] Task started: Blastn
[2023-06-28 20:41:05,596] [INFO] Running command: blastn -query GCA_020832515.1_ASM2083251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/reference_markers.fasta -out GCA_020832515.1_ASM2083251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:41:06,426] [INFO] Task succeeded: Blastn
[2023-06-28 20:41:06,432] [INFO] Selected 24 target genomes.
[2023-06-28 20:41:06,432] [INFO] Target genome list was writen to GCA_020832515.1_ASM2083251v1_genomic.fna/target_genomes.txt
[2023-06-28 20:41:06,434] [INFO] Task started: fastANI
[2023-06-28 20:41:06,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e292d0c-8588-48af-836a-0919bbdf988a/GCA_020832515.1_ASM2083251v1_genomic.fna.gz --refList GCA_020832515.1_ASM2083251v1_genomic.fna/target_genomes.txt --output GCA_020832515.1_ASM2083251v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:41:24,904] [INFO] Task succeeded: fastANI
[2023-06-28 20:41:24,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:41:24,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:41:24,925] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:41:24,925] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:41:24,926] [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
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2939	326	1164	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.2757	349	1164	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.2025	334	1164	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.1822	343	1164	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.0922	370	1164	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	77.9352	319	1164	95	below_threshold
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	77.9201	320	1164	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.906	330	1164	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.8657	331	1164	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	77.8606	352	1164	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7555	369	1164	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7233	269	1164	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	77.597	294	1164	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.5447	296	1164	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	77.4018	302	1164	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	77.3771	305	1164	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	77.3431	295	1164	95	below_threshold
Flavimaricola marinus	strain=CECT 8899	GCA_900184895.1	1819565	1819565	type	True	77.3402	304	1164	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	77.3339	298	1164	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	77.3129	306	1164	95	below_threshold
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	77.2832	344	1164	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.2821	327	1164	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.2525	307	1164	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.1996	225	1164	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:41:24,928] [INFO] DFAST Taxonomy check result was written to GCA_020832515.1_ASM2083251v1_genomic.fna/tc_result.tsv
[2023-06-28 20:41:24,929] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:41:24,929] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:41:24,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/checkm_data
[2023-06-28 20:41:24,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:41:24,976] [INFO] Task started: CheckM
[2023-06-28 20:41:24,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020832515.1_ASM2083251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020832515.1_ASM2083251v1_genomic.fna/checkm_input GCA_020832515.1_ASM2083251v1_genomic.fna/checkm_result
[2023-06-28 20:42:02,101] [INFO] Task succeeded: CheckM
[2023-06-28 20:42:02,103] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.53%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 20:42:02,131] [INFO] ===== Completeness check finished =====
[2023-06-28 20:42:02,132] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:42:02,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020832515.1_ASM2083251v1_genomic.fna/markers.fasta)
[2023-06-28 20:42:02,132] [INFO] Task started: Blastn
[2023-06-28 20:42:02,133] [INFO] Running command: blastn -query GCA_020832515.1_ASM2083251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf97967a0-857d-49e4-b28c-664050765279/dqc_reference/reference_markers_gtdb.fasta -out GCA_020832515.1_ASM2083251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:42:03,404] [INFO] Task succeeded: Blastn
[2023-06-28 20:42:03,410] [INFO] Selected 29 target genomes.
[2023-06-28 20:42:03,410] [INFO] Target genome list was writen to GCA_020832515.1_ASM2083251v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:42:03,421] [INFO] Task started: fastANI
[2023-06-28 20:42:03,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e292d0c-8588-48af-836a-0919bbdf988a/GCA_020832515.1_ASM2083251v1_genomic.fna.gz --refList GCA_020832515.1_ASM2083251v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020832515.1_ASM2083251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:42:22,688] [INFO] Task succeeded: fastANI
[2023-06-28 20:42:22,715] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:42:22,715] [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_009993005.1	s__JAACUH01 sp009993005	79.1279	461	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
GCA_001314655.1	s__Salibaculum sp001314655	78.4751	411	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649175.1	s__Rhodovulum strictum	78.2815	364	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	78.1962	321	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600975.2	s__Limimaricola hongkongensis	78.1924	335	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.0574	373	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	78.0436	320	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	77.9323	365	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	77.8851	387	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	77.8515	353	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCA_014859945.1	s__UBA1943 sp014859945	77.85	299	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	77.8246	254	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	77.766	277	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_009920775.1	s__Marivivens sp009920775	77.7474	204	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.7388	327	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	77.7205	340	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	77.7182	363	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	77.6436	342	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	77.6049	294	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	77.5573	262	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004145845.1	s__Marivivens sp004145845	77.5473	297	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	77.5365	306	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016278295.1	s__Roseovarius sp016278295	77.4041	238	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116585.1	s__Albibacillus kandeliae	77.3778	288	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792925.1	s__Gemmobacter sp016792925	77.3135	267	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	77.3038	307	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.2077	293	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116005.1	s__Poseidonocella sedimentorum	77.1116	232	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042605.1	s__IMCC34051 sp013042605	77.0474	209	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	99.10	98.86	0.88	0.86	4	-
--------------------------------------------------------------------------------
[2023-06-28 20:42:22,718] [INFO] GTDB search result was written to GCA_020832515.1_ASM2083251v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:42:22,719] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:42:22,725] [INFO] DFAST_QC result json was written to GCA_020832515.1_ASM2083251v1_genomic.fna/dqc_result.json
[2023-06-28 20:42:22,725] [INFO] DFAST_QC completed!
[2023-06-28 20:42:22,725] [INFO] Total running time: 0h1m31s