[2024-01-24 13:37:27,961] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference
[2024-01-24 13:37:29,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,178] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,178] [INFO] Running command: gunzip -c /var/lib/cwl/stg81dce24e-c700-4d7b-97ed-47b4e4d6b991/GCF_013340935.1_ASM1334093v1_genomic.fna.gz | prodigal -d GCF_013340935.1_ASM1334093v1_genomic.fna/cds.fna -a GCF_013340935.1_ASM1334093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:53,003] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:53,003] [INFO] Task started: HMMsearch
[2024-01-24 13:37:53,004] [INFO] Running command: hmmsearch --tblout GCF_013340935.1_ASM1334093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/reference_markers.hmm GCF_013340935.1_ASM1334093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:53,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:53,385] [INFO] Found 6/6 markers.
[2024-01-24 13:37:53,452] [INFO] Query marker FASTA was written to GCF_013340935.1_ASM1334093v1_genomic.fna/markers.fasta
[2024-01-24 13:37:53,453] [INFO] Task started: Blastn
[2024-01-24 13:37:53,453] [INFO] Running command: blastn -query GCF_013340935.1_ASM1334093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/reference_markers.fasta -out GCF_013340935.1_ASM1334093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:54,492] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:54,497] [INFO] Selected 12 target genomes.
[2024-01-24 13:37:54,498] [INFO] Target genome list was writen to GCF_013340935.1_ASM1334093v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:54,700] [INFO] Task started: fastANI
[2024-01-24 13:37:54,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg81dce24e-c700-4d7b-97ed-47b4e4d6b991/GCF_013340935.1_ASM1334093v1_genomic.fna.gz --refList GCF_013340935.1_ASM1334093v1_genomic.fna/target_genomes.txt --output GCF_013340935.1_ASM1334093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:17,200] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:17,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:17,202] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:17,218] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:38:17,218] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:38:17,218] [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 melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	100.0	2570	2578	95	inconclusive
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	99.9938	2562	2578	95	inconclusive
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	95.4124	2206	2578	95	inconclusive
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	91.9369	2027	2578	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	91.1995	1759	2578	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	89.8855	1758	2578	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	89.8054	1684	2578	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.7005	1374	2578	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.5702	1235	2578	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	82.44	1223	2578	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.8182	657	2578	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.6125	577	2578	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:17,220] [INFO] DFAST Taxonomy check result was written to GCF_013340935.1_ASM1334093v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:17,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:17,222] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:17,222] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/checkm_data
[2024-01-24 13:38:17,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:17,296] [INFO] Task started: CheckM
[2024-01-24 13:38:17,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340935.1_ASM1334093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340935.1_ASM1334093v1_genomic.fna/checkm_input GCF_013340935.1_ASM1334093v1_genomic.fna/checkm_result
[2024-01-24 13:39:34,819] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:34,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:34,847] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:34,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:34,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340935.1_ASM1334093v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:34,848] [INFO] Task started: Blastn
[2024-01-24 13:39:34,848] [INFO] Running command: blastn -query GCF_013340935.1_ASM1334093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a5567e9-af58-4f18-94d2-d9671d4a359a/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340935.1_ASM1334093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:36,842] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:36,847] [INFO] Selected 12 target genomes.
[2024-01-24 13:39:36,847] [INFO] Target genome list was writen to GCF_013340935.1_ASM1334093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:37,055] [INFO] Task started: fastANI
[2024-01-24 13:39:37,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg81dce24e-c700-4d7b-97ed-47b4e4d6b991/GCF_013340935.1_ASM1334093v1_genomic.fna.gz --refList GCF_013340935.1_ASM1334093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340935.1_ASM1334093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:01,776] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:01,789] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:01,789] [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_013340935.1	s__Azospirillum melinis	100.0	2570	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	conclusive
GCF_003116035.1	s__Azospirillum sp003116035	94.949	2191	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	91.939	2027	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	91.6058	1939	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004923315.1	s__Azospirillum sp003116065	91.1606	1923	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_008364795.1	s__Azospirillum oryzae	91.1549	1764	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_900177515.1	s__Azospirillum oryzae_A	91.0589	1933	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	90.9815	2031	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364825.1	s__Azospirillum sp008364825	90.0509	1820	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCF_000283655.1	s__Azospirillum lipoferum_C	90.0371	1761	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639105.2	s__Azospirillum humicireducens	89.8836	1758	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	89.8327	1681	2578	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:01,794] [INFO] GTDB search result was written to GCF_013340935.1_ASM1334093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:01,794] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:01,801] [INFO] DFAST_QC result json was written to GCF_013340935.1_ASM1334093v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:01,801] [INFO] DFAST_QC completed!
[2024-01-24 13:40:01,801] [INFO] Total running time: 0h2m34s