[2024-01-24 12:06:23,034] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:23,037] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:23,037] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference
[2024-01-24 12:06:24,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:24,304] [INFO] Task started: Prodigal
[2024-01-24 12:06:24,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b29bf17-0f69-4a7f-b8e3-8ab50fa0b75d/GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna.gz | prodigal -d GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/cds.fna -a GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:35,320] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:35,320] [INFO] Task started: HMMsearch
[2024-01-24 12:06:35,321] [INFO] Running command: hmmsearch --tblout GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/reference_markers.hmm GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,587] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,620] [INFO] Query marker FASTA was written to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/markers.fasta
[2024-01-24 12:06:35,620] [INFO] Task started: Blastn
[2024-01-24 12:06:35,620] [INFO] Running command: blastn -query GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/reference_markers.fasta -out GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:36,534] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:36,539] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:36,539] [INFO] Target genome list was writen to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/target_genomes.txt
[2024-01-24 12:06:36,547] [INFO] Task started: fastANI
[2024-01-24 12:06:36,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b29bf17-0f69-4a7f-b8e3-8ab50fa0b75d/GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna.gz --refList GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/target_genomes.txt --output GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,958] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,974] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:53,974] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:53,974] [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
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	100.0	1227	1228	95	conclusive
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	78.9302	457	1228	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	78.8757	443	1228	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.8609	276	1228	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	77.8022	274	1228	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.6748	274	1228	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.5448	285	1228	95	below_threshold
Mesorhizobium alhagi	strain=CCNWXJ12-2	GCA_000236565.2	475067	475067	type	True	77.5308	274	1228	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	77.5155	242	1228	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.4801	262	1228	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	77.4742	258	1228	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	77.4617	263	1228	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	77.4423	282	1228	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	77.2977	276	1228	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.2949	261	1228	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	77.227	214	1228	95	below_threshold
Nitratireductor indicus	strain=C115	GCA_000300515.1	721133	721133	type	True	77.2195	169	1228	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	77.0345	125	1228	95	below_threshold
Brucella melitensis	strain=16M	GCA_000250795.2	29459	29459	suspected-type	True	76.8239	124	1228	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	76.5779	112	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,976] [INFO] DFAST Taxonomy check result was written to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,977] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,977] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/checkm_data
[2024-01-24 12:06:53,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:54,015] [INFO] Task started: CheckM
[2024-01-24 12:06:54,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/checkm_input GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/checkm_result
[2024-01-24 12:07:27,808] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:27,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:27,829] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:27,829] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:27,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/markers.fasta)
[2024-01-24 12:07:27,830] [INFO] Task started: Blastn
[2024-01-24 12:07:27,830] [INFO] Running command: blastn -query GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c602e8-1af8-4e1a-9a9c-14ad1a9c0e09/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:29,377] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:29,382] [INFO] Selected 11 target genomes.
[2024-01-24 12:07:29,382] [INFO] Target genome list was writen to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:29,391] [INFO] Task started: fastANI
[2024-01-24 12:07:29,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b29bf17-0f69-4a7f-b8e3-8ab50fa0b75d/GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna.gz --refList GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/target_genomes_gtdb.txt --output GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:38,673] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:38,683] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:38,683] [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_004331745.1	s__Oricola cellulosilytica	99.9936	1223	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014904745.1	s__Oricola sp014904745	79.3478	570	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698425.1	s__Oricola sp002698425	78.9948	476	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	78.8465	446	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	78.7878	437	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191375.1	s__Paramesorhizobium sp014191375	77.8076	235	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	77.6748	274	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
GCF_012911015.1	s__Aliihoeflea sp012911015	77.5456	230	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aliihoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236565.1	s__Pseudaminobacter alhagi	77.5308	274	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	77.2873	194	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518985.1	s__Chelativorans sp000518985	77.2129	153	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Chelativorans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:38,685] [INFO] GTDB search result was written to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:38,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:38,689] [INFO] DFAST_QC result json was written to GCF_019966575.1_O_cellulosilytica_JCM19534_genomic.fna/dqc_result.json
[2024-01-24 12:07:38,689] [INFO] DFAST_QC completed!
[2024-01-24 12:07:38,689] [INFO] Total running time: 0h1m16s