[2024-01-24 13:50:10,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,342] [INFO] DQC Reference Directory: /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference
[2024-01-24 13:50:11,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,526] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg205d1f26-3b26-44a6-a732-0ac5a51cf1be/GCF_006152115.1_ASM615211v1_genomic.fna.gz | prodigal -d GCF_006152115.1_ASM615211v1_genomic.fna/cds.fna -a GCF_006152115.1_ASM615211v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:25,394] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:25,395] [INFO] Task started: HMMsearch
[2024-01-24 13:50:25,395] [INFO] Running command: hmmsearch --tblout GCF_006152115.1_ASM615211v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/reference_markers.hmm GCF_006152115.1_ASM615211v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:25,658] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:25,659] [INFO] Found 6/6 markers.
[2024-01-24 13:50:25,697] [INFO] Query marker FASTA was written to GCF_006152115.1_ASM615211v1_genomic.fna/markers.fasta
[2024-01-24 13:50:25,698] [INFO] Task started: Blastn
[2024-01-24 13:50:25,698] [INFO] Running command: blastn -query GCF_006152115.1_ASM615211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/reference_markers.fasta -out GCF_006152115.1_ASM615211v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:26,511] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:26,518] [INFO] Selected 16 target genomes.
[2024-01-24 13:50:26,519] [INFO] Target genome list was writen to GCF_006152115.1_ASM615211v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:26,540] [INFO] Task started: fastANI
[2024-01-24 13:50:26,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg205d1f26-3b26-44a6-a732-0ac5a51cf1be/GCF_006152115.1_ASM615211v1_genomic.fna.gz --refList GCF_006152115.1_ASM615211v1_genomic.fna/target_genomes.txt --output GCF_006152115.1_ASM615211v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:38,525] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,526] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:38,526] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:38,538] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:38,538] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:38,538] [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
Rubellimicrobium rubrum	strain=YIM 131921	GCA_006152115.1	2585369	2585369	type	True	100.0	1487	1489	95	conclusive
Rubellimicrobium roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	82.2608	831	1489	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	82.0001	750	1489	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	81.4191	755	1489	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.3588	406	1489	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.2874	403	1489	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.1594	333	1489	95	below_threshold
Rubellimicrobium thermophilum	strain=DSM 16684	GCA_000442315.1	295419	295419	type	True	78.1336	386	1489	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.067	375	1489	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9271	318	1489	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9102	311	1489	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5272	259	1489	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.3208	302	1489	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	77.2472	257	1489	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.1957	258	1489	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.127	196	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,540] [INFO] DFAST Taxonomy check result was written to GCF_006152115.1_ASM615211v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:38,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:38,541] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:38,541] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/checkm_data
[2024-01-24 13:50:38,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:38,590] [INFO] Task started: CheckM
[2024-01-24 13:50:38,591] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006152115.1_ASM615211v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006152115.1_ASM615211v1_genomic.fna/checkm_input GCF_006152115.1_ASM615211v1_genomic.fna/checkm_result
[2024-01-24 13:51:19,330] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:19,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:19,345] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:19,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:19,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006152115.1_ASM615211v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:19,346] [INFO] Task started: Blastn
[2024-01-24 13:51:19,346] [INFO] Running command: blastn -query GCF_006152115.1_ASM615211v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8d4c599-2ce8-4ac3-a5d5-a229cbdeefca/dqc_reference/reference_markers_gtdb.fasta -out GCF_006152115.1_ASM615211v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:20,539] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:20,542] [INFO] Selected 8 target genomes.
[2024-01-24 13:51:20,543] [INFO] Target genome list was writen to GCF_006152115.1_ASM615211v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:20,556] [INFO] Task started: fastANI
[2024-01-24 13:51:20,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg205d1f26-3b26-44a6-a732-0ac5a51cf1be/GCF_006152115.1_ASM615211v1_genomic.fna.gz --refList GCF_006152115.1_ASM615211v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006152115.1_ASM615211v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:28,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:28,063] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:28,063] [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_006152115.1	s__Rubellimicrobium rubrum	100.0	1487	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017916275.1	s__Rubellimicrobium sp017916275	82.3759	791	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006152145.1	s__Rubellimicrobium roseum	82.2891	828	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872975.1	s__Rubellimicrobium aerolatum	82.0098	749	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	81.3946	758	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805995.1	s__Rubellimicrobium sp902805995	81.0941	486	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	78.377	404	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993005.1	s__JAACUH01 sp009993005	77.6829	319	1489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAACUH01	95.0	99.57	99.57	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:28,065] [INFO] GTDB search result was written to GCF_006152115.1_ASM615211v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:28,066] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:28,070] [INFO] DFAST_QC result json was written to GCF_006152115.1_ASM615211v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:28,070] [INFO] DFAST_QC completed!
[2024-01-24 13:51:28,070] [INFO] Total running time: 0h1m18s