[2024-01-24 12:54:22,459] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,462] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference
[2024-01-24 12:54:24,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:24,005] [INFO] Task started: Prodigal
[2024-01-24 12:54:24,005] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f89a03c-8741-4a6d-9700-ebea571b30dc/GCF_006376685.1_ASM637668v1_genomic.fna.gz | prodigal -d GCF_006376685.1_ASM637668v1_genomic.fna/cds.fna -a GCF_006376685.1_ASM637668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:38,472] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:38,473] [INFO] Task started: HMMsearch
[2024-01-24 12:54:38,473] [INFO] Running command: hmmsearch --tblout GCF_006376685.1_ASM637668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/reference_markers.hmm GCF_006376685.1_ASM637668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:38,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:38,795] [INFO] Found 6/6 markers.
[2024-01-24 12:54:38,839] [INFO] Query marker FASTA was written to GCF_006376685.1_ASM637668v1_genomic.fna/markers.fasta
[2024-01-24 12:54:38,839] [INFO] Task started: Blastn
[2024-01-24 12:54:38,839] [INFO] Running command: blastn -query GCF_006376685.1_ASM637668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/reference_markers.fasta -out GCF_006376685.1_ASM637668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:39,632] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:39,637] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:39,637] [INFO] Target genome list was writen to GCF_006376685.1_ASM637668v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:39,647] [INFO] Task started: fastANI
[2024-01-24 12:54:39,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f89a03c-8741-4a6d-9700-ebea571b30dc/GCF_006376685.1_ASM637668v1_genomic.fna.gz --refList GCF_006376685.1_ASM637668v1_genomic.fna/target_genomes.txt --output GCF_006376685.1_ASM637668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:59,552] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:59,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:59,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:59,569] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:59,569] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:59,569] [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	90.0751	1292	1566	95	below_threshold
Brucella tritici	strain=LMG 18957	GCA_008932295.1	94626	94626	type	True	83.0373	954	1566	95	below_threshold
Brucella anthropi	strain=NCTC12168	GCA_900454235.1	529	529	type	True	82.9766	973	1566	95	below_threshold
Brucella anthropi	strain=ATCC 49188	GCA_000017405.1	529	529	type	True	82.9575	981	1566	95	below_threshold
Brucella intermedia	strain=LMG 3301	GCA_000182645.1	94625	94625	suspected-type	True	82.8268	962	1566	95	below_threshold
Brucella intermedia	strain=NCTC12171	GCA_900454225.1	94625	94625	suspected-type	True	82.8095	962	1566	95	below_threshold
Brucella daejeonensis	strain=DSM 26944	GCA_014199265.1	659015	659015	type	True	82.767	889	1566	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	82.2685	760	1566	95	below_threshold
Brucella melitensis	strain=16M	GCA_000007125.1	29459	29459	suspected-type	True	82.1685	760	1566	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	82.1351	759	1566	95	below_threshold
Brucella melitensis	strain=16M	GCA_000250795.2	29459	29459	suspected-type	True	82.0999	759	1566	95	below_threshold
Brucella pseudogrignonensis	strain=CCUG 30717	GCA_002252525.1	419475	419475	type	True	80.7005	808	1566	95	below_threshold
Pseudochrobactrum algeriensis		GCA_907164595.1	2834768	2834768	type	True	77.5339	318	1566	95	below_threshold
Pseudochrobactrum algeriensis		GCA_018436245.1	2834768	2834768	type	True	77.5339	318	1566	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	77.4861	335	1566	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	77.457	339	1566	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	77.4228	291	1566	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.3733	324	1566	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.3426	289	1566	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	77.2802	304	1566	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.9714	258	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:59,571] [INFO] DFAST Taxonomy check result was written to GCF_006376685.1_ASM637668v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:59,572] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:59,572] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:59,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/checkm_data
[2024-01-24 12:54:59,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:59,622] [INFO] Task started: CheckM
[2024-01-24 12:54:59,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006376685.1_ASM637668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006376685.1_ASM637668v1_genomic.fna/checkm_input GCF_006376685.1_ASM637668v1_genomic.fna/checkm_result
[2024-01-24 12:55:43,556] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:43,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:43,582] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:43,582] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:43,583] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006376685.1_ASM637668v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:43,583] [INFO] Task started: Blastn
[2024-01-24 12:55:43,583] [INFO] Running command: blastn -query GCF_006376685.1_ASM637668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54542bbf-5c0f-4ffe-8c40-9c511c9aa7c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_006376685.1_ASM637668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:44,859] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:44,864] [INFO] Selected 5 target genomes.
[2024-01-24 12:55:44,864] [INFO] Target genome list was writen to GCF_006376685.1_ASM637668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:44,869] [INFO] Task started: fastANI
[2024-01-24 12:55:44,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f89a03c-8741-4a6d-9700-ebea571b30dc/GCF_006376685.1_ASM637668v1_genomic.fna.gz --refList GCF_006376685.1_ASM637668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006376685.1_ASM637668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:51,628] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:51,638] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:51,638] [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	100.0	1564	1566	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	91.1005	1265	1566	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	90.0489	1295	1566	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	-
GCF_014138095.1	s__Ochrobactrum_B sp014138095	90.0077	1301	1566	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	-
GCA_900465685.1	s__Ochrobactrum_B sp900465685	89.9766	1287	1566	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	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:51,641] [INFO] GTDB search result was written to GCF_006376685.1_ASM637668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:51,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:51,645] [INFO] DFAST_QC result json was written to GCF_006376685.1_ASM637668v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:51,645] [INFO] DFAST_QC completed!
[2024-01-24 12:55:51,645] [INFO] Total running time: 0h1m29s