[2024-01-24 14:05:53,719] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:53,728] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:53,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference
[2024-01-24 14:05:55,098] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:55,099] [INFO] Task started: Prodigal
[2024-01-24 14:05:55,099] [INFO] Running command: gunzip -c /var/lib/cwl/stgfafcd5e2-451c-4db6-b713-5ce5b384d9be/GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/cds.fna -a GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:06,854] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:06,855] [INFO] Task started: HMMsearch
[2024-01-24 14:06:06,855] [INFO] Running command: hmmsearch --tblout GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/reference_markers.hmm GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:07,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:07,185] [INFO] Found 6/6 markers.
[2024-01-24 14:06:07,226] [INFO] Query marker FASTA was written to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 14:06:07,227] [INFO] Task started: Blastn
[2024-01-24 14:06:07,227] [INFO] Running command: blastn -query GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/reference_markers.fasta -out GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:08,422] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:08,425] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:08,426] [INFO] Target genome list was writen to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 14:06:08,430] [INFO] Task started: fastANI
[2024-01-24 14:06:08,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgfafcd5e2-451c-4db6-b713-5ce5b384d9be/GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna.gz --refList GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:20,956] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:20,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:20,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:20,967] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:20,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:20,967] [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 soesokkakensis	strain=CECT 8367	GCA_900172345.1	1343159	1343159	type	True	100.0	1289	1291	95	conclusive
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	99.9767	1250	1291	95	conclusive
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	87.8063	888	1291	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	87.7825	884	1291	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	87.7535	916	1291	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	87.0022	899	1291	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	86.2606	909	1291	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.8443	426	1291	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.8341	431	1291	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6968	420	1291	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2814	360	1291	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.5202	336	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:20,969] [INFO] DFAST Taxonomy check result was written to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 14:06:20,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:20,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:20,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/checkm_data
[2024-01-24 14:06:20,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:21,014] [INFO] Task started: CheckM
[2024-01-24 14:06:21,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/checkm_input GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 14:06:58,441] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:58,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:58,463] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:58,464] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:58,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 14:06:58,465] [INFO] Task started: Blastn
[2024-01-24 14:06:58,465] [INFO] Running command: blastn -query GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ef6c6d0-c729-4855-b5a7-38c5ba1b517c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:00,597] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:00,600] [INFO] Selected 6 target genomes.
[2024-01-24 14:07:00,600] [INFO] Target genome list was writen to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:00,609] [INFO] Task started: fastANI
[2024-01-24 14:07:00,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgfafcd5e2-451c-4db6-b713-5ce5b384d9be/GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna.gz --refList GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:06,895] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:06,907] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:06,908] [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_900172345.1	s__Limimaricola soesokkakensis	100.0	1289	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000600975.2	s__Limimaricola hongkongensis	87.8214	887	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014195545.1	s__Limimaricola variabilis	87.7751	914	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	87.6735	897	1291	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466965.1	s__Limimaricola cinnabarinus	87.0057	898	1291	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	86.2245	911	1291	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 14:07:06,910] [INFO] GTDB search result was written to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:06,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:06,918] [INFO] DFAST_QC result json was written to GCF_900172345.1_L.soesokkakensis_CECT8376_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 14:07:06,918] [INFO] DFAST_QC completed!
[2024-01-24 14:07:06,919] [INFO] Total running time: 0h1m13s