[2024-01-24 11:43:34,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:34,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:34,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference
[2024-01-24 11:43:36,184] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,185] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,186] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b2b4bf0-e159-443f-ba6f-4239dec898cf/GCF_000600975.2_Lokhon_genomic.fna.gz | prodigal -d GCF_000600975.2_Lokhon_genomic.fna/cds.fna -a GCF_000600975.2_Lokhon_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:45,526] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:45,526] [INFO] Task started: HMMsearch
[2024-01-24 11:43:45,527] [INFO] Running command: hmmsearch --tblout GCF_000600975.2_Lokhon_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/reference_markers.hmm GCF_000600975.2_Lokhon_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:45,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:45,771] [INFO] Found 6/6 markers.
[2024-01-24 11:43:45,801] [INFO] Query marker FASTA was written to GCF_000600975.2_Lokhon_genomic.fna/markers.fasta
[2024-01-24 11:43:45,801] [INFO] Task started: Blastn
[2024-01-24 11:43:45,801] [INFO] Running command: blastn -query GCF_000600975.2_Lokhon_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/reference_markers.fasta -out GCF_000600975.2_Lokhon_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:46,860] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:46,865] [INFO] Selected 12 target genomes.
[2024-01-24 11:43:46,865] [INFO] Target genome list was writen to GCF_000600975.2_Lokhon_genomic.fna/target_genomes.txt
[2024-01-24 11:43:46,949] [INFO] Task started: fastANI
[2024-01-24 11:43:46,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b2b4bf0-e159-443f-ba6f-4239dec898cf/GCF_000600975.2_Lokhon_genomic.fna.gz --refList GCF_000600975.2_Lokhon_genomic.fna/target_genomes.txt --output GCF_000600975.2_Lokhon_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:43:56,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:43:56,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:43:56,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:43:56,534] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:43:56,534] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:43:56,535] [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
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	100.0	1060	1060	95	conclusive
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	99.989	1051	1060	95	conclusive
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	87.9469	872	1060	95	below_threshold
Limimaricola soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	87.9012	878	1060	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	87.2774	814	1060	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	87.2235	846	1060	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	86.9202	859	1060	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.8069	440	1060	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.6593	373	1060	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.4889	400	1060	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.8652	357	1060	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.7887	366	1060	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:43:56,536] [INFO] DFAST Taxonomy check result was written to GCF_000600975.2_Lokhon_genomic.fna/tc_result.tsv
[2024-01-24 11:43:56,537] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:43:56,537] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:43:56,537] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/checkm_data
[2024-01-24 11:43:56,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:43:56,571] [INFO] Task started: CheckM
[2024-01-24 11:43:56,571] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000600975.2_Lokhon_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000600975.2_Lokhon_genomic.fna/checkm_input GCF_000600975.2_Lokhon_genomic.fna/checkm_result
[2024-01-24 11:44:30,684] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:30,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,705] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:30,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:30,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000600975.2_Lokhon_genomic.fna/markers.fasta)
[2024-01-24 11:44:30,707] [INFO] Task started: Blastn
[2024-01-24 11:44:30,707] [INFO] Running command: blastn -query GCF_000600975.2_Lokhon_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4ec1737-2667-4de6-a1e1-db01427b6905/dqc_reference/reference_markers_gtdb.fasta -out GCF_000600975.2_Lokhon_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:32,755] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:32,759] [INFO] Selected 6 target genomes.
[2024-01-24 11:44:32,760] [INFO] Target genome list was writen to GCF_000600975.2_Lokhon_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:32,802] [INFO] Task started: fastANI
[2024-01-24 11:44:32,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b2b4bf0-e159-443f-ba6f-4239dec898cf/GCF_000600975.2_Lokhon_genomic.fna.gz --refList GCF_000600975.2_Lokhon_genomic.fna/target_genomes_gtdb.txt --output GCF_000600975.2_Lokhon_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:38,394] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:38,401] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:38,402] [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_000600975.2	s__Limimaricola hongkongensis	100.0	1060	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002723615.1	s__Limimaricola cinnabarinus_B	89.2259	851	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172345.1	s__Limimaricola soesokkakensis	87.9273	876	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000466965.1	s__Limimaricola cinnabarinus	87.2541	816	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	87.2065	848	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	86.8848	862	1060	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:38,403] [INFO] GTDB search result was written to GCF_000600975.2_Lokhon_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:38,404] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:38,407] [INFO] DFAST_QC result json was written to GCF_000600975.2_Lokhon_genomic.fna/dqc_result.json
[2024-01-24 11:44:38,407] [INFO] DFAST_QC completed!
[2024-01-24 11:44:38,407] [INFO] Total running time: 0h1m3s