[2024-01-24 12:05:26,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference
[2024-01-24 12:05:30,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,684] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,684] [INFO] Running command: gunzip -c /var/lib/cwl/stg73d07f2a-a98a-4a91-9c19-d14a01c8ad80/GCF_004010155.1_ASM401015v1_genomic.fna.gz | prodigal -d GCF_004010155.1_ASM401015v1_genomic.fna/cds.fna -a GCF_004010155.1_ASM401015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:43,952] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:43,952] [INFO] Task started: HMMsearch
[2024-01-24 12:05:43,952] [INFO] Running command: hmmsearch --tblout GCF_004010155.1_ASM401015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/reference_markers.hmm GCF_004010155.1_ASM401015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:44,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:44,248] [INFO] Found 6/6 markers.
[2024-01-24 12:05:44,303] [INFO] Query marker FASTA was written to GCF_004010155.1_ASM401015v1_genomic.fna/markers.fasta
[2024-01-24 12:05:44,303] [INFO] Task started: Blastn
[2024-01-24 12:05:44,304] [INFO] Running command: blastn -query GCF_004010155.1_ASM401015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/reference_markers.fasta -out GCF_004010155.1_ASM401015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:45,375] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:45,379] [INFO] Selected 32 target genomes.
[2024-01-24 12:05:45,379] [INFO] Target genome list was writen to GCF_004010155.1_ASM401015v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:45,416] [INFO] Task started: fastANI
[2024-01-24 12:05:45,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d07f2a-a98a-4a91-9c19-d14a01c8ad80/GCF_004010155.1_ASM401015v1_genomic.fna.gz --refList GCF_004010155.1_ASM401015v1_genomic.fna/target_genomes.txt --output GCF_004010155.1_ASM401015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:09,020] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:09,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:09,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:09,045] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:09,045] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:09,045] [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
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.9977	578	1546	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.9411	604	1546	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.4098	477	1546	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_001720585.1	445629	445629	type	True	79.3138	505	1546	95	below_threshold
Cereibacter johrii	strain=JA192	GCA_003046325.1	445629	445629	type	True	79.2805	532	1546	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	79.265	505	1546	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	79.2122	503	1546	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	79.0637	543	1546	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	79.0529	537	1546	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	79.0491	525	1546	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	79.0381	539	1546	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	78.9983	544	1546	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.9591	523	1546	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	78.9427	520	1546	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.7878	455	1546	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.757	451	1546	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.7477	465	1546	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	78.6378	484	1546	95	below_threshold
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	78.4481	435	1546	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	78.4239	435	1546	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	78.4121	398	1546	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.3872	416	1546	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	78.3595	436	1546	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.1627	434	1546	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	78.1128	443	1546	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.1066	492	1546	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	78.0522	457	1546	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.7582	329	1546	95	below_threshold
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	77.6177	317	1546	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	77.6068	318	1546	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5997	330	1546	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.408	319	1546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:09,047] [INFO] DFAST Taxonomy check result was written to GCF_004010155.1_ASM401015v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:09,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:09,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:09,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/checkm_data
[2024-01-24 12:06:09,049] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:09,101] [INFO] Task started: CheckM
[2024-01-24 12:06:09,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004010155.1_ASM401015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004010155.1_ASM401015v1_genomic.fna/checkm_input GCF_004010155.1_ASM401015v1_genomic.fna/checkm_result
[2024-01-24 12:06:50,160] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:50,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,186] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:50,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:50,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004010155.1_ASM401015v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:50,187] [INFO] Task started: Blastn
[2024-01-24 12:06:50,187] [INFO] Running command: blastn -query GCF_004010155.1_ASM401015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg133ce6ad-d209-4f76-8d3a-6743d8a4af59/dqc_reference/reference_markers_gtdb.fasta -out GCF_004010155.1_ASM401015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,332] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,335] [INFO] Selected 23 target genomes.
[2024-01-24 12:06:52,336] [INFO] Target genome list was writen to GCF_004010155.1_ASM401015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:52,354] [INFO] Task started: fastANI
[2024-01-24 12:06:52,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg73d07f2a-a98a-4a91-9c19-d14a01c8ad80/GCF_004010155.1_ASM401015v1_genomic.fna.gz --refList GCF_004010155.1_ASM401015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004010155.1_ASM401015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:10,208] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:10,231] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:10,232] [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_004010155.1	s__Solirhodobacter olei	100.0	1543	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016124615.1	s__Solirhodobacter sp016124615	80.6695	781	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871005.1	s__Acidimangrovimonas sediminis	79.7239	715	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106675.1	s__Acidimangrovimonas indica	79.6486	602	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_002407205.1	s__Cereibacter_A sp002407205	79.6132	526	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043545.1	s__JAAKGP01 sp011043545	79.5264	585	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	79.5133	451	1546	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	79.3845	534	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.3271	528	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	79.3171	429	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCA_002280515.1	s__Albidovulum sp002280515	79.3122	537	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008271465.1	s__Tabrizicola flagellata	78.9741	517	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.8725	467	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	78.7791	456	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_003053725.1	s__Rhodovulum kholense	78.7762	462	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_003944755.1	s__Rhodovulum robiginosum	78.7575	464	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002073975.1	s__Rhodovulum sp002073975	78.6042	442	1546	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	78.5529	502	1546	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_014640115.1	s__Muriiphilus lacisalsi	78.4578	430	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278325.1	s__JADQCB01 sp016278325	78.1346	373	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JADQCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	78.1312	323	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551745.1	s__Rhodobaculum sp003551745	78.1067	294	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314685.1	s__HLUCCA09 sp001314685	77.9749	411	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:10,233] [INFO] GTDB search result was written to GCF_004010155.1_ASM401015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:10,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:10,240] [INFO] DFAST_QC result json was written to GCF_004010155.1_ASM401015v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:10,240] [INFO] DFAST_QC completed!
[2024-01-24 12:07:10,240] [INFO] Total running time: 0h1m44s