[2024-01-25 17:44:50,539] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:50,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:50,541] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference
[2024-01-25 17:44:51,670] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:51,671] [INFO] Task started: Prodigal
[2024-01-25 17:44:51,671] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c62c506-435d-49e4-acbb-c8247a251b48/GCF_025995295.1_ASM2599529v1_genomic.fna.gz | prodigal -d GCF_025995295.1_ASM2599529v1_genomic.fna/cds.fna -a GCF_025995295.1_ASM2599529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:01,293] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:01,293] [INFO] Task started: HMMsearch
[2024-01-25 17:45:01,293] [INFO] Running command: hmmsearch --tblout GCF_025995295.1_ASM2599529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/reference_markers.hmm GCF_025995295.1_ASM2599529v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:01,496] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:01,497] [INFO] Found 6/6 markers.
[2024-01-25 17:45:01,534] [INFO] Query marker FASTA was written to GCF_025995295.1_ASM2599529v1_genomic.fna/markers.fasta
[2024-01-25 17:45:01,534] [INFO] Task started: Blastn
[2024-01-25 17:45:01,534] [INFO] Running command: blastn -query GCF_025995295.1_ASM2599529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/reference_markers.fasta -out GCF_025995295.1_ASM2599529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:02,232] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:02,236] [INFO] Selected 15 target genomes.
[2024-01-25 17:45:02,236] [INFO] Target genome list was writen to GCF_025995295.1_ASM2599529v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:02,245] [INFO] Task started: fastANI
[2024-01-25 17:45:02,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c62c506-435d-49e4-acbb-c8247a251b48/GCF_025995295.1_ASM2599529v1_genomic.fna.gz --refList GCF_025995295.1_ASM2599529v1_genomic.fna/target_genomes.txt --output GCF_025995295.1_ASM2599529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:12,309] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:12,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:12,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:12,317] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:12,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:12,318] [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
Acidocella aminolytica	strain=DSM 11237	GCA_900129125.1	33998	33998	type	True	99.9427	1135	1145	95	conclusive
Acidocella facilis	strain=ATCC 35904	GCA_000687875.1	525	525	type	True	80.8454	540	1145	95	below_threshold
Acidocella aromatica	strain=DSM 27026	GCA_014201825.1	1303579	1303579	type	True	79.1005	341	1145	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.8577	171	1145	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.3514	160	1145	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4046	130	1145	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	76.286	96	1145	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	76.2417	69	1145	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.1618	78	1145	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.9527	109	1145	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:12,319] [INFO] DFAST Taxonomy check result was written to GCF_025995295.1_ASM2599529v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:12,320] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:12,320] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:12,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/checkm_data
[2024-01-25 17:45:12,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:12,362] [INFO] Task started: CheckM
[2024-01-25 17:45:12,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995295.1_ASM2599529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995295.1_ASM2599529v1_genomic.fna/checkm_input GCF_025995295.1_ASM2599529v1_genomic.fna/checkm_result
[2024-01-25 17:45:43,379] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:43,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:43,403] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:43,403] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:43,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995295.1_ASM2599529v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:43,404] [INFO] Task started: Blastn
[2024-01-25 17:45:43,404] [INFO] Running command: blastn -query GCF_025995295.1_ASM2599529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd5f5e87-5eb0-4453-9ea2-a6f2d480ede1/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995295.1_ASM2599529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:44,754] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:44,757] [INFO] Selected 13 target genomes.
[2024-01-25 17:45:44,757] [INFO] Target genome list was writen to GCF_025995295.1_ASM2599529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:44,772] [INFO] Task started: fastANI
[2024-01-25 17:45:44,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c62c506-435d-49e4-acbb-c8247a251b48/GCF_025995295.1_ASM2599529v1_genomic.fna.gz --refList GCF_025995295.1_ASM2599529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995295.1_ASM2599529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:52,420] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:52,429] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:52,429] [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_900129125.1	s__Acidocella aminolytica	99.9427	1135	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_018971725.1	s__Acidocella sp018971725	81.2464	365	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687875.1	s__Acidocella facilis	80.8562	538	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	98.02	98.02	0.93	0.93	2	-
GCA_018971565.1	s__Acidocella sp018971565	80.4455	353	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971905.1	s__Acidocella sp018971905	80.3349	287	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201825.1	s__Acidocella aromatica	79.0806	342	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164135.1	s__Acidocella sp003164135	77.4256	216	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	99.77	99.73	0.97	0.95	5	-
GCA_013044125.1	s__Acidocella sp013044125	77.2955	209	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516935.1	s__Acetobacter farinalis	76.3638	55	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279355.1	s__Acidiphilium sp002279355	76.3082	71	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidiphilium	95.0	99.80	99.77	0.93	0.92	3	-
GCF_014199195.1	s__Roseomonas_B alkaliterrae	76.286	96	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	99.89	99.89	0.97	0.97	2	-
GCA_903844785.1	s__Roseomonas_B sp903844785	75.594	56	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:45:52,430] [INFO] GTDB search result was written to GCF_025995295.1_ASM2599529v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:52,431] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:52,435] [INFO] DFAST_QC result json was written to GCF_025995295.1_ASM2599529v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:52,435] [INFO] DFAST_QC completed!
[2024-01-25 17:45:52,435] [INFO] Total running time: 0h1m2s