[2024-01-24 11:27:19,106] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:19,108] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:19,108] [INFO] DQC Reference Directory: /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference
[2024-01-24 11:27:20,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:20,296] [INFO] Task started: Prodigal
[2024-01-24 11:27:20,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg18b3ec34-1d71-4754-87b1-9773721827a8/GCF_003664555.1_ASM366455v1_genomic.fna.gz | prodigal -d GCF_003664555.1_ASM366455v1_genomic.fna/cds.fna -a GCF_003664555.1_ASM366455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:35,445] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:35,446] [INFO] Task started: HMMsearch
[2024-01-24 11:27:35,446] [INFO] Running command: hmmsearch --tblout GCF_003664555.1_ASM366455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/reference_markers.hmm GCF_003664555.1_ASM366455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:35,726] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:35,728] [INFO] Found 6/6 markers.
[2024-01-24 11:27:35,773] [INFO] Query marker FASTA was written to GCF_003664555.1_ASM366455v1_genomic.fna/markers.fasta
[2024-01-24 11:27:35,773] [INFO] Task started: Blastn
[2024-01-24 11:27:35,773] [INFO] Running command: blastn -query GCF_003664555.1_ASM366455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/reference_markers.fasta -out GCF_003664555.1_ASM366455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:36,555] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:36,559] [INFO] Selected 21 target genomes.
[2024-01-24 11:27:36,559] [INFO] Target genome list was writen to GCF_003664555.1_ASM366455v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:36,570] [INFO] Task started: fastANI
[2024-01-24 11:27:36,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b3ec34-1d71-4754-87b1-9773721827a8/GCF_003664555.1_ASM366455v1_genomic.fna.gz --refList GCF_003664555.1_ASM366455v1_genomic.fna/target_genomes.txt --output GCF_003664555.1_ASM366455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:56,970] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:56,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:56,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:56,993] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:27:56,993] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:27:56,993] [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 haematophila	strain=CCUG 38531	GCA_005938105.1	419474	419474	type	True	90.2659	1331	1655	95	below_threshold
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	83.2852	962	1655	95	below_threshold
Brucella pecoris	strain=DSM 23868	GCA_014197065.1	867683	867683	type	True	83.1166	981	1655	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	83.0818	989	1655	95	below_threshold
Brucella pecoris	strain=08RB2639	GCA_006376675.1	867683	867683	type	True	82.9954	992	1655	95	below_threshold
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	82.9884	997	1655	95	below_threshold
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	82.9153	1008	1655	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	82.7279	918	1655	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	82.1517	758	1655	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	80.8398	806	1655	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_003049685.2	571256	571256	type	True	80.7229	856	1655	95	below_threshold
Brucella pituitosa	strain=CCUG 50899	GCA_008801705.1	571256	571256	type	True	80.7201	839	1655	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	77.7247	319	1655	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.6831	315	1655	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	77.6765	316	1655	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.6726	316	1655	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	77.5623	369	1655	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	77.4283	358	1655	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.22	357	1655	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.2026	308	1655	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.0366	263	1655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:56,995] [INFO] DFAST Taxonomy check result was written to GCF_003664555.1_ASM366455v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:56,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:56,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:56,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/checkm_data
[2024-01-24 11:27:56,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:57,042] [INFO] Task started: CheckM
[2024-01-24 11:27:57,042] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664555.1_ASM366455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664555.1_ASM366455v1_genomic.fna/checkm_input GCF_003664555.1_ASM366455v1_genomic.fna/checkm_result
[2024-01-24 11:28:42,488] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:42,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:42,509] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:42,510] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:42,510] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664555.1_ASM366455v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:42,510] [INFO] Task started: Blastn
[2024-01-24 11:28:42,511] [INFO] Running command: blastn -query GCF_003664555.1_ASM366455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1018b812-02e1-4e8f-bccb-d3ff174299d7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664555.1_ASM366455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:43,833] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:43,837] [INFO] Selected 5 target genomes.
[2024-01-24 11:28:43,837] [INFO] Target genome list was writen to GCF_003664555.1_ASM366455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:43,843] [INFO] Task started: fastANI
[2024-01-24 11:28:43,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg18b3ec34-1d71-4754-87b1-9773721827a8/GCF_003664555.1_ASM366455v1_genomic.fna.gz --refList GCF_003664555.1_ASM366455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664555.1_ASM366455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:50,752] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:50,762] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:50,762] [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_006376685.1	s__Ochrobactrum_B teleogrylli	98.1596	1408	1655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.13	98.09	0.91	0.90	5	conclusive
GCF_016427605.1	s__Ochrobactrum_B sp016427605	91.3687	1360	1655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938105.1	s__Ochrobactrum_B haematophila	90.2439	1333	1655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	98.61	97.38	0.92	0.84	3	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	90.2322	1338	1655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	99.22	99.21	0.91	0.91	3	-
GCF_014138095.1	s__Ochrobactrum_B sp014138095	90.203	1383	1655	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Ochrobactrum_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:50,765] [INFO] GTDB search result was written to GCF_003664555.1_ASM366455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:50,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:50,769] [INFO] DFAST_QC result json was written to GCF_003664555.1_ASM366455v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:50,769] [INFO] DFAST_QC completed!
[2024-01-24 11:28:50,769] [INFO] Total running time: 0h1m32s