[2024-01-24 10:47:11,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:11,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:11,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference
[2024-01-24 10:47:16,944] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:16,945] [INFO] Task started: Prodigal
[2024-01-24 10:47:16,946] [INFO] Running command: gunzip -c /var/lib/cwl/stgf153b29b-1f78-44b1-bda5-aebdfaa578e1/GCF_001017435.1_ASM101743v1_genomic.fna.gz | prodigal -d GCF_001017435.1_ASM101743v1_genomic.fna/cds.fna -a GCF_001017435.1_ASM101743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:57,986] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:57,987] [INFO] Task started: HMMsearch
[2024-01-24 10:47:57,987] [INFO] Running command: hmmsearch --tblout GCF_001017435.1_ASM101743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/reference_markers.hmm GCF_001017435.1_ASM101743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:58,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:58,298] [INFO] Found 6/6 markers.
[2024-01-24 10:47:58,347] [INFO] Query marker FASTA was written to GCF_001017435.1_ASM101743v1_genomic.fna/markers.fasta
[2024-01-24 10:47:58,347] [INFO] Task started: Blastn
[2024-01-24 10:47:58,347] [INFO] Running command: blastn -query GCF_001017435.1_ASM101743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/reference_markers.fasta -out GCF_001017435.1_ASM101743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:59,372] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:59,376] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:59,377] [INFO] Target genome list was writen to GCF_001017435.1_ASM101743v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:59,385] [INFO] Task started: fastANI
[2024-01-24 10:47:59,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgf153b29b-1f78-44b1-bda5-aebdfaa578e1/GCF_001017435.1_ASM101743v1_genomic.fna.gz --refList GCF_001017435.1_ASM101743v1_genomic.fna/target_genomes.txt --output GCF_001017435.1_ASM101743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:18,163] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:18,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:18,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:18,179] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:18,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:18,180] [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
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	100.0	2157	2158	95	conclusive
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	82.1866	802	2158	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	82.1637	813	2158	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	82.0952	828	2158	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.6393	526	2158	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.548	619	2158	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_016583525.1	28068	28068	suspected-type	True	79.504	652	2158	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4942	548	2158	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.4607	638	2158	95	below_threshold
Rubrivivax gelatinosus	strain=DSM 1709	GCA_004340905.1	28068	28068	suspected-type	True	79.3947	679	2158	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.1933	566	2158	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.0711	695	2158	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.0572	562	2158	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.991	705	2158	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.9658	599	2158	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.79	629	2158	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	78.6018	632	2158	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:18,181] [INFO] DFAST Taxonomy check result was written to GCF_001017435.1_ASM101743v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:18,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:18,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:18,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/checkm_data
[2024-01-24 10:48:18,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:18,252] [INFO] Task started: CheckM
[2024-01-24 10:48:18,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001017435.1_ASM101743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001017435.1_ASM101743v1_genomic.fna/checkm_input GCF_001017435.1_ASM101743v1_genomic.fna/checkm_result
[2024-01-24 10:51:10,255] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:10,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:10,279] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:10,280] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:10,280] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001017435.1_ASM101743v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:10,280] [INFO] Task started: Blastn
[2024-01-24 10:51:10,281] [INFO] Running command: blastn -query GCF_001017435.1_ASM101743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f2635e0-9ff7-4020-a61b-289268094a89/dqc_reference/reference_markers_gtdb.fasta -out GCF_001017435.1_ASM101743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:12,465] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:12,469] [INFO] Selected 18 target genomes.
[2024-01-24 10:51:12,470] [INFO] Target genome list was writen to GCF_001017435.1_ASM101743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:12,495] [INFO] Task started: fastANI
[2024-01-24 10:51:12,495] [INFO] Running command: fastANI --query /var/lib/cwl/stgf153b29b-1f78-44b1-bda5-aebdfaa578e1/GCF_001017435.1_ASM101743v1_genomic.fna.gz --refList GCF_001017435.1_ASM101743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001017435.1_ASM101743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:32,773] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:32,793] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:32,794] [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
GCA_001017435.1	s__Polyangium_A brachysporum	100.0	2157	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polyangium_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015476235.1	s__Schlegelella thermodepolymerans	82.1099	824	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Schlegelella	95.0	99.89	99.68	0.98	0.95	4	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	80.7038	756	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002930615.1	s__Zhizhongheella caldifontis	80.4805	636	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Zhizhongheella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983795.1	s__Piscinibacter sp017983795	80.3652	678	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	97.66	96.21	0.89	0.79	4	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	80.3458	797	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000800095.1	s__Rhizobacter sp000800095	80.1349	856	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142965.1	s__Rhizobacter sp900142965	80.0627	873	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	80.0624	770	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017795745.1	s__Piscinibacter sp017795745	79.9494	712	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	79.4626	665	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCA_019234815.1	s__WAJ17 sp019234815	79.3426	415	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__WAJ17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255905.1	s__PBB1 sp002255905	79.3183	427	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PBB1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	79.1617	628	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCA_002205125.1	s__Mitsuaria noduli	79.0369	637	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001295865.1	s__Rubrivivax sp001295865	78.9346	590	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.99	99.99	0.99	0.99	2	-
GCA_004210455.1	s__Mitsuaria sp004210455	78.8852	627	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161115.1	s__Variovorax sp017161115	78.5203	601	2158	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:51:32,797] [INFO] GTDB search result was written to GCF_001017435.1_ASM101743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:32,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:32,803] [INFO] DFAST_QC result json was written to GCF_001017435.1_ASM101743v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:32,803] [INFO] DFAST_QC completed!
[2024-01-24 10:51:32,803] [INFO] Total running time: 0h4m21s