[2024-01-24 13:58:10,924] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference
[2024-01-24 13:58:12,204] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,205] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,206] [INFO] Running command: gunzip -c /var/lib/cwl/stgb570b3d1-ea28-4567-8b9e-16604640f07e/GCF_008932295.1_ASM893229v1_genomic.fna.gz | prodigal -d GCF_008932295.1_ASM893229v1_genomic.fna/cds.fna -a GCF_008932295.1_ASM893229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:28,659] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:28,659] [INFO] Task started: HMMsearch
[2024-01-24 13:58:28,660] [INFO] Running command: hmmsearch --tblout GCF_008932295.1_ASM893229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/reference_markers.hmm GCF_008932295.1_ASM893229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:29,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:29,044] [INFO] Found 6/6 markers.
[2024-01-24 13:58:29,094] [INFO] Query marker FASTA was written to GCF_008932295.1_ASM893229v1_genomic.fna/markers.fasta
[2024-01-24 13:58:29,095] [INFO] Task started: Blastn
[2024-01-24 13:58:29,095] [INFO] Running command: blastn -query GCF_008932295.1_ASM893229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/reference_markers.fasta -out GCF_008932295.1_ASM893229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:29,866] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:29,870] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:29,870] [INFO] Target genome list was writen to GCF_008932295.1_ASM893229v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:29,875] [INFO] Task started: fastANI
[2024-01-24 13:58:29,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgb570b3d1-ea28-4567-8b9e-16604640f07e/GCF_008932295.1_ASM893229v1_genomic.fna.gz --refList GCF_008932295.1_ASM893229v1_genomic.fna/target_genomes.txt --output GCF_008932295.1_ASM893229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:42,992] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:42,992] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:42,993] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:43,007] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:43,007] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:43,008] [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
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	100.0	1684	1689	95	conclusive
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	91.6636	1333	1689	95	below_threshold
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	91.6554	1328	1689	95	below_threshold
Brucella pecoris	strain=08RB2639	GCA_006376675.1	867683	867683	type	True	89.4042	1303	1689	95	below_threshold
Brucella pecoris	strain=DSM 23868	GCA_014197065.1	867683	867683	type	True	89.3714	1308	1689	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	88.1004	1248	1689	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	88.0876	1244	1689	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.7306	278	1689	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.6785	280	1689	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	77.4771	290	1689	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.0745	275	1689	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.9492	222	1689	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,009] [INFO] DFAST Taxonomy check result was written to GCF_008932295.1_ASM893229v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:43,010] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:43,010] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:43,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/checkm_data
[2024-01-24 13:58:43,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:43,065] [INFO] Task started: CheckM
[2024-01-24 13:58:43,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008932295.1_ASM893229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008932295.1_ASM893229v1_genomic.fna/checkm_input GCF_008932295.1_ASM893229v1_genomic.fna/checkm_result
[2024-01-24 13:59:33,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:33,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:33,534] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:33,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:33,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008932295.1_ASM893229v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:33,536] [INFO] Task started: Blastn
[2024-01-24 13:59:33,536] [INFO] Running command: blastn -query GCF_008932295.1_ASM893229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97e49584-6885-47b8-9cee-fff381319296/dqc_reference/reference_markers_gtdb.fasta -out GCF_008932295.1_ASM893229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:34,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:34,865] [INFO] Selected 10 target genomes.
[2024-01-24 13:59:34,865] [INFO] Target genome list was writen to GCF_008932295.1_ASM893229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:34,878] [INFO] Task started: fastANI
[2024-01-24 13:59:34,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgb570b3d1-ea28-4567-8b9e-16604640f07e/GCF_008932295.1_ASM893229v1_genomic.fna.gz --refList GCF_008932295.1_ASM893229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008932295.1_ASM893229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:47,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:47,984] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:47,984] [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_008932295.1	s__Ochrobactrum tritici	100.0	1684	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	98.18	96.73	0.91	0.84	6	conclusive
GCF_902825325.1	s__Ochrobactrum sp003176975	93.7048	1303	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.64	97.64	0.88	0.88	2	-
GCF_000017405.1	s__Ochrobactrum anthropi	91.6484	1328	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.11	96.94	0.89	0.83	55	-
GCA_012103075.1	s__Ochrobactrum cytisi	90.9359	1335	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.518	98.45	98.45	0.94	0.94	2	-
GCA_012103035.1	s__Ochrobactrum oryzae	90.5756	1238	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.03	98.38	0.88	0.83	3	-
GCF_006376675.1	s__Ochrobactrum pecoris	89.4061	1302	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.97	99.94	1.00	1.00	3	-
GCF_006345815.1	s__Ochrobactrum sp006345815	88.5993	1179	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470195.1	s__Ochrobactrum sp900470195	88.2233	1237	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	99.22	97.63	0.95	0.85	7	-
GCF_000182645.1	s__Ochrobactrum intermedium	88.1113	1247	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	97.99	97.16	0.92	0.84	56	-
GCA_900473915.1	s__Ochrobactrum sp900473915	87.7514	1124	1689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:47,989] [INFO] GTDB search result was written to GCF_008932295.1_ASM893229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:47,990] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:47,995] [INFO] DFAST_QC result json was written to GCF_008932295.1_ASM893229v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:47,996] [INFO] DFAST_QC completed!
[2024-01-24 13:59:47,996] [INFO] Total running time: 0h1m37s