[2024-01-24 14:03:03,051] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:03,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:03,053] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference
[2024-01-24 14:03:04,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:04,351] [INFO] Task started: Prodigal
[2024-01-24 14:03:04,351] [INFO] Running command: gunzip -c /var/lib/cwl/stg41b097eb-b211-45a6-887a-545090edf273/GCF_008364795.1_ASM836479v1_genomic.fna.gz | prodigal -d GCF_008364795.1_ASM836479v1_genomic.fna/cds.fna -a GCF_008364795.1_ASM836479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:24,681] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:24,682] [INFO] Task started: HMMsearch
[2024-01-24 14:03:24,682] [INFO] Running command: hmmsearch --tblout GCF_008364795.1_ASM836479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/reference_markers.hmm GCF_008364795.1_ASM836479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:25,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:25,161] [INFO] Found 6/6 markers.
[2024-01-24 14:03:25,219] [INFO] Query marker FASTA was written to GCF_008364795.1_ASM836479v1_genomic.fna/markers.fasta
[2024-01-24 14:03:25,220] [INFO] Task started: Blastn
[2024-01-24 14:03:25,220] [INFO] Running command: blastn -query GCF_008364795.1_ASM836479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/reference_markers.fasta -out GCF_008364795.1_ASM836479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:26,266] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:26,269] [INFO] Selected 15 target genomes.
[2024-01-24 14:03:26,270] [INFO] Target genome list was writen to GCF_008364795.1_ASM836479v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:26,280] [INFO] Task started: fastANI
[2024-01-24 14:03:26,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg41b097eb-b211-45a6-887a-545090edf273/GCF_008364795.1_ASM836479v1_genomic.fna.gz --refList GCF_008364795.1_ASM836479v1_genomic.fna/target_genomes.txt --output GCF_008364795.1_ASM836479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:53,438] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:53,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:53,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:53,454] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:53,454] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:53,454] [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 oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	100.0	2231	2233	95	conclusive
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	91.4885	1727	2233	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	91.4641	1786	2233	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	91.3128	1729	2233	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	91.2854	1779	2233	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	90.4236	1586	2233	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	90.2168	1652	2233	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	89.1121	1647	2233	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	89.101	1656	2233	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	87.1449	1473	2233	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	82.8224	1129	2233	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.6163	1199	2233	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.5295	1155	2233	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.913	598	2233	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5677	495	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:53,457] [INFO] DFAST Taxonomy check result was written to GCF_008364795.1_ASM836479v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:53,457] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:53,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:53,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/checkm_data
[2024-01-24 14:03:53,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:53,519] [INFO] Task started: CheckM
[2024-01-24 14:03:53,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008364795.1_ASM836479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008364795.1_ASM836479v1_genomic.fna/checkm_input GCF_008364795.1_ASM836479v1_genomic.fna/checkm_result
[2024-01-24 14:05:01,747] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:01,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:01,774] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:01,774] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:01,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008364795.1_ASM836479v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:01,775] [INFO] Task started: Blastn
[2024-01-24 14:05:01,775] [INFO] Running command: blastn -query GCF_008364795.1_ASM836479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ae7a3a1-d90f-47e0-aa27-83ca5bc70f8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008364795.1_ASM836479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:03,938] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:03,942] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:03,943] [INFO] Target genome list was writen to GCF_008364795.1_ASM836479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:03,953] [INFO] Task started: fastANI
[2024-01-24 14:05:03,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg41b097eb-b211-45a6-887a-545090edf273/GCF_008364795.1_ASM836479v1_genomic.fna.gz --refList GCF_008364795.1_ASM836479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008364795.1_ASM836479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:24,644] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:24,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:24,663] [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_008364795.1	s__Azospirillum oryzae	100.0	2231	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	conclusive
GCF_004923315.1	s__Azospirillum sp003116065	94.7654	1936	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_900177515.1	s__Azospirillum oryzae_A	94.2722	1836	2233	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	91.4714	1729	2233	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	91.2069	1673	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016595245.1	s__Azospirillum sp016595245	90.9349	1753	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	90.827	1653	2233	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	90.7476	1723	2233	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	90.4315	1585	2233	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	90.2057	1653	2233	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 14:05:24,665] [INFO] GTDB search result was written to GCF_008364795.1_ASM836479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:24,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:24,672] [INFO] DFAST_QC result json was written to GCF_008364795.1_ASM836479v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:24,673] [INFO] DFAST_QC completed!
[2024-01-24 14:05:24,673] [INFO] Total running time: 0h2m22s