[2024-01-24 14:23:01,324] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:01,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:01,325] [INFO] DQC Reference Directory: /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference
[2024-01-24 14:23:02,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:02,552] [INFO] Task started: Prodigal
[2024-01-24 14:23:02,552] [INFO] Running command: gunzip -c /var/lib/cwl/stg11786342-869e-4cc7-8f78-164df72e11b3/GCF_013340925.1_ASM1334092v1_genomic.fna.gz | prodigal -d GCF_013340925.1_ASM1334092v1_genomic.fna/cds.fna -a GCF_013340925.1_ASM1334092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:18,239] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:18,240] [INFO] Task started: HMMsearch
[2024-01-24 14:23:18,240] [INFO] Running command: hmmsearch --tblout GCF_013340925.1_ASM1334092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/reference_markers.hmm GCF_013340925.1_ASM1334092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:18,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:18,611] [INFO] Found 6/6 markers.
[2024-01-24 14:23:18,686] [INFO] Query marker FASTA was written to GCF_013340925.1_ASM1334092v1_genomic.fna/markers.fasta
[2024-01-24 14:23:18,687] [INFO] Task started: Blastn
[2024-01-24 14:23:18,687] [INFO] Running command: blastn -query GCF_013340925.1_ASM1334092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/reference_markers.fasta -out GCF_013340925.1_ASM1334092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:19,775] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:19,779] [INFO] Selected 12 target genomes.
[2024-01-24 14:23:19,779] [INFO] Target genome list was writen to GCF_013340925.1_ASM1334092v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:19,784] [INFO] Task started: fastANI
[2024-01-24 14:23:19,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg11786342-869e-4cc7-8f78-164df72e11b3/GCF_013340925.1_ASM1334092v1_genomic.fna.gz --refList GCF_013340925.1_ASM1334092v1_genomic.fna/target_genomes.txt --output GCF_013340925.1_ASM1334092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:38,413] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:38,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:38,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:38,432] [INFO] Found 12 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:23:38,432] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:38,432] [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 formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	100.0	1762	1784	95	inconclusive
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	95.1888	1615	1784	95	inconclusive
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	95.1703	1607	1784	95	inconclusive
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	95.1304	1581	1784	95	inconclusive
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	95.1294	1609	1784	95	inconclusive
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	94.7678	1608	1784	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	94.7493	1608	1784	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	94.6102	1597	1784	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	94.1373	1534	1784	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.0906	856	1784	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.4239	585	1784	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.0759	216	1784	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:38,438] [INFO] DFAST Taxonomy check result was written to GCF_013340925.1_ASM1334092v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:38,439] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:38,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:38,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/checkm_data
[2024-01-24 14:23:38,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:38,507] [INFO] Task started: CheckM
[2024-01-24 14:23:38,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013340925.1_ASM1334092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013340925.1_ASM1334092v1_genomic.fna/checkm_input GCF_013340925.1_ASM1334092v1_genomic.fna/checkm_result
[2024-01-24 14:24:31,207] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:31,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:31,240] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:31,241] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:31,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013340925.1_ASM1334092v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:31,241] [INFO] Task started: Blastn
[2024-01-24 14:24:31,242] [INFO] Running command: blastn -query GCF_013340925.1_ASM1334092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee492904-8b35-4f13-86b5-ba96f5767cb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013340925.1_ASM1334092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:33,355] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:33,358] [INFO] Selected 8 target genomes.
[2024-01-24 14:24:33,358] [INFO] Target genome list was writen to GCF_013340925.1_ASM1334092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:33,369] [INFO] Task started: fastANI
[2024-01-24 14:24:33,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg11786342-869e-4cc7-8f78-164df72e11b3/GCF_013340925.1_ASM1334092v1_genomic.fna.gz --refList GCF_013340925.1_ASM1334092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013340925.1_ASM1334092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:47,711] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:47,724] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:47,724] [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	95.1703	1607	1784	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	94.7709	1606	1784	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	94.7689	1593	1784	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	94.5362	1608	1784	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_014192915.1	s__Azospirillum sp014192915	94.3921	1592	1784	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	94.3351	1516	1784	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_007827815.1	s__Azospirillum brasilense_C	94.306	1569	1784	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_002245955.1	s__Azospirillum brasilense_A	94.0773	1557	1784	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:47,726] [INFO] GTDB search result was written to GCF_013340925.1_ASM1334092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:47,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:47,737] [INFO] DFAST_QC result json was written to GCF_013340925.1_ASM1334092v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:47,737] [INFO] DFAST_QC completed!
[2024-01-24 14:24:47,737] [INFO] Total running time: 0h1m46s