[2024-01-24 14:56:22,693] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:22,696] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:22,696] [INFO] DQC Reference Directory: /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference
[2024-01-24 14:56:26,554] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,556] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg21f6fc80-2810-43cb-9db1-000a91d50083/GCF_002027385.1_ASM202738v1_genomic.fna.gz | prodigal -d GCF_002027385.1_ASM202738v1_genomic.fna/cds.fna -a GCF_002027385.1_ASM202738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:48,154] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:48,154] [INFO] Task started: HMMsearch
[2024-01-24 14:56:48,154] [INFO] Running command: hmmsearch --tblout GCF_002027385.1_ASM202738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/reference_markers.hmm GCF_002027385.1_ASM202738v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:48,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:48,681] [INFO] Found 6/6 markers.
[2024-01-24 14:56:48,744] [INFO] Query marker FASTA was written to GCF_002027385.1_ASM202738v1_genomic.fna/markers.fasta
[2024-01-24 14:56:48,744] [INFO] Task started: Blastn
[2024-01-24 14:56:48,744] [INFO] Running command: blastn -query GCF_002027385.1_ASM202738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/reference_markers.fasta -out GCF_002027385.1_ASM202738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:49,758] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:49,763] [INFO] Selected 15 target genomes.
[2024-01-24 14:56:49,763] [INFO] Target genome list was writen to GCF_002027385.1_ASM202738v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:49,773] [INFO] Task started: fastANI
[2024-01-24 14:56:49,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg21f6fc80-2810-43cb-9db1-000a91d50083/GCF_002027385.1_ASM202738v1_genomic.fna.gz --refList GCF_002027385.1_ASM202738v1_genomic.fna/target_genomes.txt --output GCF_002027385.1_ASM202738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:10,488] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:10,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:10,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:10,508] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:57:10,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:10,508] [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
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	100.0	2218	2229	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	99.9924	2221	2229	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	99.9546	2014	2229	95	conclusive
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	99.9442	2181	2229	95	conclusive
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	94.9214	1568	2229	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	94.8979	1941	2229	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	94.0075	1749	2229	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	80.9196	967	2229	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.8309	261	2229	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.1883	233	2229	95	below_threshold
Acidovorax avenae subsp. avenae	strain=ATCC 19860	GCA_000176855.2	80870	80867	suspected-type	True	75.8106	249	2229	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	75.692	263	2229	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	75.6485	278	2229	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	75.5999	284	2229	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	75.5998	233	2229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:10,511] [INFO] DFAST Taxonomy check result was written to GCF_002027385.1_ASM202738v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:10,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:10,512] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:10,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/checkm_data
[2024-01-24 14:57:10,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:10,587] [INFO] Task started: CheckM
[2024-01-24 14:57:10,587] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002027385.1_ASM202738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002027385.1_ASM202738v1_genomic.fna/checkm_input GCF_002027385.1_ASM202738v1_genomic.fna/checkm_result
[2024-01-24 14:58:17,011] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:17,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:17,042] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:17,043] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:17,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002027385.1_ASM202738v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:17,045] [INFO] Task started: Blastn
[2024-01-24 14:58:17,045] [INFO] Running command: blastn -query GCF_002027385.1_ASM202738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga18b2e5d-f4a9-4a80-bbfa-7d2ac0849a89/dqc_reference/reference_markers_gtdb.fasta -out GCF_002027385.1_ASM202738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:18,806] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:18,810] [INFO] Selected 14 target genomes.
[2024-01-24 14:58:18,810] [INFO] Target genome list was writen to GCF_002027385.1_ASM202738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:18,827] [INFO] Task started: fastANI
[2024-01-24 14:58:18,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg21f6fc80-2810-43cb-9db1-000a91d50083/GCF_002027385.1_ASM202738v1_genomic.fna.gz --refList GCF_002027385.1_ASM202738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002027385.1_ASM202738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:42,175] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:42,191] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:42,192] [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_001315015.1	s__Azospirillum brasilense	99.9546	2014	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	conclusive
GCF_003119195.2	s__Azospirillum baldaniorum	94.9577	1973	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_008365405.1	s__Azospirillum brasilense_D	94.5055	1897	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	94.4287	1936	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_007827815.1	s__Azospirillum brasilense_C	94.4147	1915	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_003349955.1	s__Azospirillum brasilense_B	94.4095	1838	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_007827795.1	s__Azospirillum brasilense_E	94.3483	1802	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_014192915.1	s__Azospirillum sp014192915	94.1179	1896	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245955.1	s__Azospirillum brasilense_A	93.9617	1862	2229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
GCF_000176855.2	s__Acidovorax_A avenae	75.8219	245	2229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	96.92	95.92	0.74	0.51	18	-
GCF_900104515.1	s__Acidovorax_A cattleyae	75.7027	263	2229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.69	99.69	0.82	0.82	2	-
GCF_000687165.1	s__Acidovorax_A oryzae	75.6685	277	2229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.2137	98.08	98.08	0.87	0.87	2	-
GCA_002397315.1	s__Acidovorax_A sp002397315	75.6143	275	2229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100305.1	s__Acidovorax_A citrulli	75.5865	232	2229	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	99.47	99.27	0.97	0.96	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:42,194] [INFO] GTDB search result was written to GCF_002027385.1_ASM202738v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:42,194] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:42,201] [INFO] DFAST_QC result json was written to GCF_002027385.1_ASM202738v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:42,202] [INFO] DFAST_QC completed!
[2024-01-24 14:58:42,202] [INFO] Total running time: 0h2m20s