[2024-01-24 11:43:25,080] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,082] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,057] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fe909ad-8c7a-4008-b95f-66f782ecd135/GCF_014653075.1_ASM1465307v1_genomic.fna.gz | prodigal -d GCF_014653075.1_ASM1465307v1_genomic.fna/cds.fna -a GCF_014653075.1_ASM1465307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:42,477] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:42,477] [INFO] Task started: HMMsearch
[2024-01-24 11:43:42,478] [INFO] Running command: hmmsearch --tblout GCF_014653075.1_ASM1465307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/reference_markers.hmm GCF_014653075.1_ASM1465307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:42,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:42,762] [INFO] Found 6/6 markers.
[2024-01-24 11:43:42,799] [INFO] Query marker FASTA was written to GCF_014653075.1_ASM1465307v1_genomic.fna/markers.fasta
[2024-01-24 11:43:42,799] [INFO] Task started: Blastn
[2024-01-24 11:43:42,799] [INFO] Running command: blastn -query GCF_014653075.1_ASM1465307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/reference_markers.fasta -out GCF_014653075.1_ASM1465307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:43,792] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:43,812] [INFO] Selected 24 target genomes.
[2024-01-24 11:43:43,813] [INFO] Target genome list was writen to GCF_014653075.1_ASM1465307v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:43,823] [INFO] Task started: fastANI
[2024-01-24 11:43:43,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fe909ad-8c7a-4008-b95f-66f782ecd135/GCF_014653075.1_ASM1465307v1_genomic.fna.gz --refList GCF_014653075.1_ASM1465307v1_genomic.fna/target_genomes.txt --output GCF_014653075.1_ASM1465307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:02,735] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:02,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:02,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:02,755] [INFO] Found 24 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:02,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:02,755] [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
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	100.0	1391	1393	95	conclusive
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	99.9811	1375	1393	95	conclusive
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	79.4185	548	1393	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	79.3645	535	1393	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	79.215	522	1393	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	79.2048	510	1393	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	79.1121	505	1393	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.1115	471	1393	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	79.0281	528	1393	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.0	502	1393	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.9128	564	1393	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	78.8494	440	1393	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.8174	512	1393	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	78.8142	477	1393	95	below_threshold
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	78.6049	477	1393	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.5531	388	1393	95	below_threshold
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	78.5455	463	1393	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	78.5399	380	1393	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	78.4469	475	1393	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	78.399	413	1393	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.3854	452	1393	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1215	411	1393	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0481	397	1393	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.8732	373	1393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:02,757] [INFO] DFAST Taxonomy check result was written to GCF_014653075.1_ASM1465307v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:02,758] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:02,758] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:02,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/checkm_data
[2024-01-24 11:44:02,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:02,832] [INFO] Task started: CheckM
[2024-01-24 11:44:02,832] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653075.1_ASM1465307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653075.1_ASM1465307v1_genomic.fna/checkm_input GCF_014653075.1_ASM1465307v1_genomic.fna/checkm_result
[2024-01-24 11:44:42,623] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:42,625] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:42,643] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:42,643] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:42,644] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653075.1_ASM1465307v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:42,644] [INFO] Task started: Blastn
[2024-01-24 11:44:42,644] [INFO] Running command: blastn -query GCF_014653075.1_ASM1465307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07476bf7-09e4-46f0-89ee-ee4b090e44b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653075.1_ASM1465307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:44,505] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:44,510] [INFO] Selected 21 target genomes.
[2024-01-24 11:44:44,510] [INFO] Target genome list was writen to GCF_014653075.1_ASM1465307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:44,526] [INFO] Task started: fastANI
[2024-01-24 11:44:44,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fe909ad-8c7a-4008-b95f-66f782ecd135/GCF_014653075.1_ASM1465307v1_genomic.fna.gz --refList GCF_014653075.1_ASM1465307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653075.1_ASM1465307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:01,304] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:01,329] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:01,329] [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_900106675.1	s__Acidimangrovimonas indica	99.9811	1375	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	99.99	99.99	1.00	0.99	3	conclusive
GCF_002871005.1	s__Acidimangrovimonas sediminis	81.9536	840	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.7941	551	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	79.7431	591	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124615.1	s__Solirhodobacter sp016124615	79.5786	607	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	79.3708	535	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_009649175.1	s__Rhodovulum strictum	79.2235	508	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	79.1122	505	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004365965.1	s__Rhodovulum visakhapatnamense	79.0068	531	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.55	98.44	0.90	0.89	5	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	78.9605	518	1393	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_015999335.1	s__Tabrizicola soli	78.8979	530	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	78.8658	451	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511785.1	s__UBA7951 sp003511785	78.7869	333	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122215.1	s__Pararhodobacter marinus	78.6687	492	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811755.1	s__Pararhodobacter sp017811755	78.6229	421	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002085925.2	s__Thioclava electrotropha	78.6004	479	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	78.542	482	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	78.4776	329	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.4444	433	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009296265.1	s__Thioclava sp009296265	78.4435	467	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCA_016278295.1	s__Roseovarius sp016278295	77.9402	333	1393	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:01,331] [INFO] GTDB search result was written to GCF_014653075.1_ASM1465307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:01,332] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:01,340] [INFO] DFAST_QC result json was written to GCF_014653075.1_ASM1465307v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:01,340] [INFO] DFAST_QC completed!
[2024-01-24 11:45:01,341] [INFO] Total running time: 0h1m36s