[2024-01-24 11:05:27,180] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,182] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,182] [INFO] DQC Reference Directory: /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference
[2024-01-24 11:05:28,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:28,468] [INFO] Task started: Prodigal
[2024-01-24 11:05:28,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg9675147b-c0d2-46ee-9825-5a78e9c560ca/GCF_018853545.1_ASM1885354v1_genomic.fna.gz | prodigal -d GCF_018853545.1_ASM1885354v1_genomic.fna/cds.fna -a GCF_018853545.1_ASM1885354v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:36,859] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:36,859] [INFO] Task started: HMMsearch
[2024-01-24 11:05:36,859] [INFO] Running command: hmmsearch --tblout GCF_018853545.1_ASM1885354v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/reference_markers.hmm GCF_018853545.1_ASM1885354v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:37,111] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:37,112] [INFO] Found 6/6 markers.
[2024-01-24 11:05:37,140] [INFO] Query marker FASTA was written to GCF_018853545.1_ASM1885354v1_genomic.fna/markers.fasta
[2024-01-24 11:05:37,140] [INFO] Task started: Blastn
[2024-01-24 11:05:37,140] [INFO] Running command: blastn -query GCF_018853545.1_ASM1885354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/reference_markers.fasta -out GCF_018853545.1_ASM1885354v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:37,888] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:37,892] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:37,892] [INFO] Target genome list was writen to GCF_018853545.1_ASM1885354v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:37,899] [INFO] Task started: fastANI
[2024-01-24 11:05:37,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg9675147b-c0d2-46ee-9825-5a78e9c560ca/GCF_018853545.1_ASM1885354v1_genomic.fna.gz --refList GCF_018853545.1_ASM1885354v1_genomic.fna/target_genomes.txt --output GCF_018853545.1_ASM1885354v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:48,588] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:48,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:48,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:48,599] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:48,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:48,599] [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
Acidithiobacillus caldus	strain=KU	GCA_018853545.1	33059	33059	type	True	100.0	819	826	95	conclusive
Acidithiobacillus caldus	strain=ATCC 51756	GCA_000175575.2	33059	33059	type	True	99.9815	822	826	95	conclusive
Acidithiobacillus caldus	strain=DSM 8584	GCA_018853615.1	33059	33059	type	True	99.8731	810	826	95	conclusive
Acidithiobacillus ferridurans	strain=ATCC 33020	GCA_018854555.1	1232575	1232575	type	True	77.5962	112	826	95	below_threshold
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	77.5687	168	826	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	77.4284	108	826	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	77.3965	123	826	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	76.9617	136	826	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	76.8551	94	826	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.8852	51	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:48,607] [INFO] DFAST Taxonomy check result was written to GCF_018853545.1_ASM1885354v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:48,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:48,608] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:48,608] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/checkm_data
[2024-01-24 11:05:48,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:48,649] [INFO] Task started: CheckM
[2024-01-24 11:05:48,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018853545.1_ASM1885354v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018853545.1_ASM1885354v1_genomic.fna/checkm_input GCF_018853545.1_ASM1885354v1_genomic.fna/checkm_result
[2024-01-24 11:06:18,337] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:18,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:18,360] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:18,360] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:18,361] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018853545.1_ASM1885354v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:18,361] [INFO] Task started: Blastn
[2024-01-24 11:06:18,362] [INFO] Running command: blastn -query GCF_018853545.1_ASM1885354v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8014a7b6-a16c-4edb-a558-710fa29843ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_018853545.1_ASM1885354v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:19,720] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:19,725] [INFO] Selected 28 target genomes.
[2024-01-24 11:06:19,725] [INFO] Target genome list was writen to GCF_018853545.1_ASM1885354v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:19,750] [INFO] Task started: fastANI
[2024-01-24 11:06:19,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg9675147b-c0d2-46ee-9825-5a78e9c560ca/GCF_018853545.1_ASM1885354v1_genomic.fna.gz --refList GCF_018853545.1_ASM1885354v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018853545.1_ASM1885354v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:35,431] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:35,442] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:35,442] [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_000175575.2	s__Acidithiobacillus_A caldus	99.9815	822	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_A	95.0	99.11	98.61	0.89	0.82	17	conclusive
GCF_018854025.1	s__UBA2486 sp018854025	77.5934	139	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	99.54	99.39	0.91	0.89	6	-
GCF_003721225.1	s__Acidithiobacillus_B sulfuriphilus	77.5633	167	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966655.1	s__Acidithiobacillus ferridurans	77.4284	108	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.15	97.49	0.87	0.83	8	-
GCF_000021485.1	s__Acidithiobacillus ferrooxidans	77.3965	123	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	98.94	96.59	0.87	0.73	15	-
GCA_002341825.1	s__UBA2486 sp002341825	77.2483	109	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__UBA2486	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018854495.1	s__Acidithiobacillus ferrooxidans_C	77.1183	115	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853935.1	s__Acidithiobacillus ferrivorans	77.0857	92	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	96.97	95.59	0.71	0.67	8	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	76.9705	95	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
GCF_010378095.1	s__Acidithiobacillus ferrianus	76.9617	136	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853465.1	s__Acidithiobacillus sp018853465	76.5248	100	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	-
GCF_002847505.1	s__Acidithiobacillus sp002847505	76.5206	101	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:35,445] [INFO] GTDB search result was written to GCF_018853545.1_ASM1885354v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:35,446] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:35,451] [INFO] DFAST_QC result json was written to GCF_018853545.1_ASM1885354v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:35,452] [INFO] DFAST_QC completed!
[2024-01-24 11:06:35,452] [INFO] Total running time: 0h1m8s