[2024-01-24 14:40:02,138] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:02,145] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:02,145] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference
[2024-01-24 14:40:03,534] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:03,534] [INFO] Task started: Prodigal
[2024-01-24 14:40:03,535] [INFO] Running command: gunzip -c /var/lib/cwl/stgbde06465-f431-4649-bd04-5e6566991412/GCF_002573965.1_ASM257396v1_genomic.fna.gz | prodigal -d GCF_002573965.1_ASM257396v1_genomic.fna/cds.fna -a GCF_002573965.1_ASM257396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:28,659] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:28,659] [INFO] Task started: HMMsearch
[2024-01-24 14:40:28,659] [INFO] Running command: hmmsearch --tblout GCF_002573965.1_ASM257396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/reference_markers.hmm GCF_002573965.1_ASM257396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:29,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:29,070] [INFO] Found 6/6 markers.
[2024-01-24 14:40:29,168] [INFO] Query marker FASTA was written to GCF_002573965.1_ASM257396v1_genomic.fna/markers.fasta
[2024-01-24 14:40:29,168] [INFO] Task started: Blastn
[2024-01-24 14:40:29,169] [INFO] Running command: blastn -query GCF_002573965.1_ASM257396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/reference_markers.fasta -out GCF_002573965.1_ASM257396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:30,364] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:30,367] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:30,368] [INFO] Target genome list was writen to GCF_002573965.1_ASM257396v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:30,377] [INFO] Task started: fastANI
[2024-01-24 14:40:30,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgbde06465-f431-4649-bd04-5e6566991412/GCF_002573965.1_ASM257396v1_genomic.fna.gz --refList GCF_002573965.1_ASM257396v1_genomic.fna/target_genomes.txt --output GCF_002573965.1_ASM257396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:56,716] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:56,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:56,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:56,728] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:40:56,728] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:40:56,728] [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 palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	100.0	2647	2648	95	inconclusive
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	95.5094	2254	2648	95	inconclusive
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	95.4838	2192	2648	95	inconclusive
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	91.9232	2052	2648	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	91.3496	1801	2648	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	90.035	1811	2648	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	89.8441	1710	2648	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.7102	1405	2648	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	82.665	1264	2648	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.5155	1269	2648	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.917	664	2648	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.3926	608	2648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:56,730] [INFO] DFAST Taxonomy check result was written to GCF_002573965.1_ASM257396v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:56,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:56,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:56,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/checkm_data
[2024-01-24 14:40:56,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:56,811] [INFO] Task started: CheckM
[2024-01-24 14:40:56,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002573965.1_ASM257396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002573965.1_ASM257396v1_genomic.fna/checkm_input GCF_002573965.1_ASM257396v1_genomic.fna/checkm_result
[2024-01-24 14:42:20,440] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:20,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:20,466] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:20,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:20,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002573965.1_ASM257396v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:20,467] [INFO] Task started: Blastn
[2024-01-24 14:42:20,467] [INFO] Running command: blastn -query GCF_002573965.1_ASM257396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5e2c746-53e1-451d-bcc3-80f840d5c8d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002573965.1_ASM257396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:22,763] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:22,767] [INFO] Selected 11 target genomes.
[2024-01-24 14:42:22,767] [INFO] Target genome list was writen to GCF_002573965.1_ASM257396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:22,776] [INFO] Task started: fastANI
[2024-01-24 14:42:22,776] [INFO] Running command: fastANI --query /var/lib/cwl/stgbde06465-f431-4649-bd04-5e6566991412/GCF_002573965.1_ASM257396v1_genomic.fna.gz --refList GCF_002573965.1_ASM257396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002573965.1_ASM257396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:47,606] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:47,615] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 14:42:47,615] [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	95.478	2193	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	inconclusive
GCF_003116035.1	s__Azospirillum sp003116035	95.2333	2255	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_008364955.1	s__Azospirillum lipoferum	91.9148	2053	2648	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	91.6538	1959	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_008364795.1	s__Azospirillum oryzae	91.3756	1798	2648	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	91.2101	1946	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	91.2059	1952	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_016595245.1	s__Azospirillum sp016595245	91.0585	2046	2648	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	90.344	1826	2648	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCF_001639105.2	s__Azospirillum humicireducens	90.0366	1812	2648	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	89.797	1716	2648	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 14:42:47,617] [INFO] GTDB search result was written to GCF_002573965.1_ASM257396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:47,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:47,632] [INFO] DFAST_QC result json was written to GCF_002573965.1_ASM257396v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:47,632] [INFO] DFAST_QC completed!
[2024-01-24 14:42:47,632] [INFO] Total running time: 0h2m45s