[2024-01-25 19:57:20,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:20,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:20,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference
[2024-01-25 19:57:21,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:21,943] [INFO] Task started: Prodigal
[2024-01-25 19:57:21,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d8b1724-2d7b-4e91-ae79-1899bb607ba6/GCF_030814845.1_ASM3081484v1_genomic.fna.gz | prodigal -d GCF_030814845.1_ASM3081484v1_genomic.fna/cds.fna -a GCF_030814845.1_ASM3081484v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:42,356] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:42,356] [INFO] Task started: HMMsearch
[2024-01-25 19:57:42,356] [INFO] Running command: hmmsearch --tblout GCF_030814845.1_ASM3081484v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/reference_markers.hmm GCF_030814845.1_ASM3081484v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:42,657] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:42,658] [INFO] Found 6/6 markers.
[2024-01-25 19:57:42,714] [INFO] Query marker FASTA was written to GCF_030814845.1_ASM3081484v1_genomic.fna/markers.fasta
[2024-01-25 19:57:42,714] [INFO] Task started: Blastn
[2024-01-25 19:57:42,714] [INFO] Running command: blastn -query GCF_030814845.1_ASM3081484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/reference_markers.fasta -out GCF_030814845.1_ASM3081484v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:43,710] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:43,712] [INFO] Selected 13 target genomes.
[2024-01-25 19:57:43,713] [INFO] Target genome list was writen to GCF_030814845.1_ASM3081484v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:43,723] [INFO] Task started: fastANI
[2024-01-25 19:57:43,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8b1724-2d7b-4e91-ae79-1899bb607ba6/GCF_030814845.1_ASM3081484v1_genomic.fna.gz --refList GCF_030814845.1_ASM3081484v1_genomic.fna/target_genomes.txt --output GCF_030814845.1_ASM3081484v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:09,184] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:09,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:09,186] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:09,195] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:09,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:09,195] [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 rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	99.9965	2474	2484	95	conclusive
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	86.1791	1511	2484	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	86.1688	1316	2484	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	86.0721	1597	2484	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	85.9824	1600	2484	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	85.9402	1532	2484	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	85.9318	1586	2484	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	85.9306	1613	2484	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	85.9278	1578	2484	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	85.9045	1549	2484	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.1377	751	2484	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.8976	254	2484	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.5318	535	2484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:09,197] [INFO] DFAST Taxonomy check result was written to GCF_030814845.1_ASM3081484v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:09,198] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:09,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:09,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/checkm_data
[2024-01-25 19:58:09,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:09,266] [INFO] Task started: CheckM
[2024-01-25 19:58:09,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814845.1_ASM3081484v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814845.1_ASM3081484v1_genomic.fna/checkm_input GCF_030814845.1_ASM3081484v1_genomic.fna/checkm_result
[2024-01-25 19:59:21,765] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:21,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:21,786] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:21,787] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:21,787] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814845.1_ASM3081484v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:21,787] [INFO] Task started: Blastn
[2024-01-25 19:59:21,787] [INFO] Running command: blastn -query GCF_030814845.1_ASM3081484v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34f8ef8f-bf79-4ff9-9680-0d95dc91e2f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814845.1_ASM3081484v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:23,897] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:23,900] [INFO] Selected 11 target genomes.
[2024-01-25 19:59:23,900] [INFO] Target genome list was writen to GCF_030814845.1_ASM3081484v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:23,914] [INFO] Task started: fastANI
[2024-01-25 19:59:23,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d8b1724-2d7b-4e91-ae79-1899bb607ba6/GCF_030814845.1_ASM3081484v1_genomic.fna.gz --refList GCF_030814845.1_ASM3081484v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814845.1_ASM3081484v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:47,521] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:47,529] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:47,529] [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_017876155.1	s__Azospirillum rugosum	99.9965	2474	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003119115.1	s__Azospirillum sp003119115	86.3848	1614	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	86.1496	1551	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365375.1	s__Azospirillum sp008365375	86.1368	1526	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	86.1118	1593	2484	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	86.0875	1581	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.48	97.48	0.91	0.91	2	-
GCF_014192915.1	s__Azospirillum sp014192915	86.0648	1563	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119195.2	s__Azospirillum baldaniorum	86.0311	1603	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_003349955.1	s__Azospirillum brasilense_B	86.0303	1492	2484	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	85.9864	1530	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.90	98.81	0.89	0.86	3	-
GCF_001315015.1	s__Azospirillum brasilense	85.9508	1530	2484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:47,530] [INFO] GTDB search result was written to GCF_030814845.1_ASM3081484v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:47,531] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:47,534] [INFO] DFAST_QC result json was written to GCF_030814845.1_ASM3081484v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:47,534] [INFO] DFAST_QC completed!
[2024-01-25 19:59:47,534] [INFO] Total running time: 0h2m27s