[2024-01-24 14:21:50,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference
[2024-01-24 14:21:52,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,279] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,279] [INFO] Running command: gunzip -c /var/lib/cwl/stgf27ce3c5-049d-412a-a587-7ed5e3cecece/GCF_006152145.1_ASM615214v1_genomic.fna.gz | prodigal -d GCF_006152145.1_ASM615214v1_genomic.fna/cds.fna -a GCF_006152145.1_ASM615214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:06,205] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:06,205] [INFO] Task started: HMMsearch
[2024-01-24 14:22:06,205] [INFO] Running command: hmmsearch --tblout GCF_006152145.1_ASM615214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/reference_markers.hmm GCF_006152145.1_ASM615214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:06,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:06,490] [INFO] Found 6/6 markers.
[2024-01-24 14:22:06,532] [INFO] Query marker FASTA was written to GCF_006152145.1_ASM615214v1_genomic.fna/markers.fasta
[2024-01-24 14:22:06,533] [INFO] Task started: Blastn
[2024-01-24 14:22:06,533] [INFO] Running command: blastn -query GCF_006152145.1_ASM615214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/reference_markers.fasta -out GCF_006152145.1_ASM615214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:07,577] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:07,585] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:07,585] [INFO] Target genome list was writen to GCF_006152145.1_ASM615214v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:07,589] [INFO] Task started: fastANI
[2024-01-24 14:22:07,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27ce3c5-049d-412a-a587-7ed5e3cecece/GCF_006152145.1_ASM615214v1_genomic.fna.gz --refList GCF_006152145.1_ASM615214v1_genomic.fna/target_genomes.txt --output GCF_006152145.1_ASM615214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:19,678] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:19,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:19,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:19,692] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:19,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:19,693] [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 roseum	strain=YIM 48858	GCA_006152145.1	687525	687525	type	True	100.0	1534	1541	95	conclusive
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	84.3361	857	1541	95	below_threshold
Rubellimicrobium mesophilum	strain=DSM 19309	GCA_000600335.2	1123067	1123067	type	True	83.6457	891	1541	95	below_threshold
Rubellimicrobium rubrum	strain=YIM 131921	GCA_006152115.1	2585369	2585369	type	True	82.0776	833	1541	95	below_threshold
Rubellimicrobium thermophilum	strain=DSM 16684	GCA_000442315.1	295419	295419	type	True	78.785	486	1541	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.6416	468	1541	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.6364	529	1541	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.5264	439	1541	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.4392	488	1541	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.4369	438	1541	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.1086	354	1541	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.7255	392	1541	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.7235	393	1541	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5841	360	1541	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:19,697] [INFO] DFAST Taxonomy check result was written to GCF_006152145.1_ASM615214v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:19,697] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:19,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:19,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/checkm_data
[2024-01-24 14:22:19,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:19,754] [INFO] Task started: CheckM
[2024-01-24 14:22:19,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006152145.1_ASM615214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006152145.1_ASM615214v1_genomic.fna/checkm_input GCF_006152145.1_ASM615214v1_genomic.fna/checkm_result
[2024-01-24 14:23:01,616] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:01,618] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:01,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:01,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:01,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006152145.1_ASM615214v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:01,637] [INFO] Task started: Blastn
[2024-01-24 14:23:01,637] [INFO] Running command: blastn -query GCF_006152145.1_ASM615214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e1ddd81-7491-4e56-a6b4-f6085c665437/dqc_reference/reference_markers_gtdb.fasta -out GCF_006152145.1_ASM615214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:03,710] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:03,715] [INFO] Selected 9 target genomes.
[2024-01-24 14:23:03,715] [INFO] Target genome list was writen to GCF_006152145.1_ASM615214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:03,722] [INFO] Task started: fastANI
[2024-01-24 14:23:03,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgf27ce3c5-049d-412a-a587-7ed5e3cecece/GCF_006152145.1_ASM615214v1_genomic.fna.gz --refList GCF_006152145.1_ASM615214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006152145.1_ASM615214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:12,508] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:12,524] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:12,524] [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_006152145.1	s__Rubellimicrobium roseum	100.0	1534	1541	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_017872975.1	s__Rubellimicrobium aerolatum	84.3358	857	1541	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	83.5886	897	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	83.2125	851	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902805995.1	s__Rubellimicrobium sp902805995	82.698	525	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006152115.1	s__Rubellimicrobium rubrum	82.1026	830	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009904055.1	s__Rubellimicrobium sp009904055	79.9072	621	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442315.1	s__Rubellimicrobium thermophilum	78.8113	483	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	78.0209	431	1541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:12,526] [INFO] GTDB search result was written to GCF_006152145.1_ASM615214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:12,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:12,532] [INFO] DFAST_QC result json was written to GCF_006152145.1_ASM615214v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:12,532] [INFO] DFAST_QC completed!
[2024-01-24 14:23:12,532] [INFO] Total running time: 0h1m22s