[2024-01-24 11:59:22,958] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:22,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:22,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference
[2024-01-24 11:59:25,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:25,652] [INFO] Task started: Prodigal
[2024-01-24 11:59:25,652] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b339f26-33ff-433e-8e77-29cc14012230/GCF_018853465.1_ASM1885346v1_genomic.fna.gz | prodigal -d GCF_018853465.1_ASM1885346v1_genomic.fna/cds.fna -a GCF_018853465.1_ASM1885346v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:33,600] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:33,600] [INFO] Task started: HMMsearch
[2024-01-24 11:59:33,601] [INFO] Running command: hmmsearch --tblout GCF_018853465.1_ASM1885346v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/reference_markers.hmm GCF_018853465.1_ASM1885346v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:33,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:33,858] [INFO] Found 6/6 markers.
[2024-01-24 11:59:33,893] [INFO] Query marker FASTA was written to GCF_018853465.1_ASM1885346v1_genomic.fna/markers.fasta
[2024-01-24 11:59:33,894] [INFO] Task started: Blastn
[2024-01-24 11:59:33,894] [INFO] Running command: blastn -query GCF_018853465.1_ASM1885346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/reference_markers.fasta -out GCF_018853465.1_ASM1885346v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:34,564] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:34,568] [INFO] Selected 19 target genomes.
[2024-01-24 11:59:34,568] [INFO] Target genome list was writen to GCF_018853465.1_ASM1885346v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:34,605] [INFO] Task started: fastANI
[2024-01-24 11:59:34,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b339f26-33ff-433e-8e77-29cc14012230/GCF_018853465.1_ASM1885346v1_genomic.fna.gz --refList GCF_018853465.1_ASM1885346v1_genomic.fna/target_genomes.txt --output GCF_018853465.1_ASM1885346v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:43,638] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:43,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:43,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:43,654] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:59:43,654] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:59:43,654] [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 thiooxidans	strain=ATCC 19377	GCA_006718285.1	930	930	suspected-type	True	80.9541	510	861	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_009662475.1	930	930	suspected-type	True	80.8815	512	861	95	below_threshold
Acidithiobacillus thiooxidans	strain=ATCC 19377	GCA_000227215.2	930	930	suspected-type	True	80.7653	470	861	95	below_threshold
Acidithiobacillus ferrooxidans	strain=ATCC 23270	GCA_000021485.1	920	920	type	True	78.2102	224	861	95	below_threshold
Acidithiobacillus ferridurans	strain=JCM 18981	GCA_003966655.1	1232575	1232575	type	True	78.0736	240	861	95	below_threshold
Acidithiobacillus ferriphilus	strain=DSM 100412	GCA_018854775.1	1689834	1689834	type	True	77.8549	189	861	95	below_threshold
Acidithiobacillus ferrianus	strain=MG	GCA_010378095.1	2678518	2678518	type	True	77.6896	202	861	95	below_threshold
Acidithiobacillus sulfuriphilus	strain=CJ-2	GCA_003721225.1	1867749	1867749	type	True	76.9571	136	861	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:43,656] [INFO] DFAST Taxonomy check result was written to GCF_018853465.1_ASM1885346v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:43,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:43,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:43,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/checkm_data
[2024-01-24 11:59:43,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:43,692] [INFO] Task started: CheckM
[2024-01-24 11:59:43,693] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018853465.1_ASM1885346v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018853465.1_ASM1885346v1_genomic.fna/checkm_input GCF_018853465.1_ASM1885346v1_genomic.fna/checkm_result
[2024-01-24 12:00:12,185] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:12,186] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:12,199] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:12,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:12,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018853465.1_ASM1885346v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:12,200] [INFO] Task started: Blastn
[2024-01-24 12:00:12,201] [INFO] Running command: blastn -query GCF_018853465.1_ASM1885346v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc98701e3-7ff3-4f76-8881-2cb1d80aa9c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_018853465.1_ASM1885346v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:13,256] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:13,262] [INFO] Selected 10 target genomes.
[2024-01-24 12:00:13,263] [INFO] Target genome list was writen to GCF_018853465.1_ASM1885346v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:13,270] [INFO] Task started: fastANI
[2024-01-24 12:00:13,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b339f26-33ff-433e-8e77-29cc14012230/GCF_018853465.1_ASM1885346v1_genomic.fna.gz --refList GCF_018853465.1_ASM1885346v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018853465.1_ASM1885346v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:19,139] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:19,154] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:19,154] [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_018853465.1	s__Acidithiobacillus sp018853465	100.0	853	861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.74	99.74	0.91	0.91	2	conclusive
GCF_002847505.1	s__Acidithiobacillus sp002847505	90.3714	650	861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015100155.1	s__Acidithiobacillus sp015100155	81.0164	521	861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	99.95	99.95	0.97	0.97	2	-
GCF_009662475.1	s__Acidithiobacillus thiooxidans	80.8979	511	861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	97.93	97.09	0.77	0.70	22	-
GCF_018853815.1	s__Acidithiobacillus sp018853815	80.7481	508	861	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidithiobacillales;f__Acidithiobacillaceae;g__Acidithiobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018853445.1	s__Acidithiobacillus sp018853445	80.4868	487	861	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 12:00:19,157] [INFO] GTDB search result was written to GCF_018853465.1_ASM1885346v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:19,158] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:19,161] [INFO] DFAST_QC result json was written to GCF_018853465.1_ASM1885346v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:19,162] [INFO] DFAST_QC completed!
[2024-01-24 12:00:19,162] [INFO] Total running time: 0h0m56s