[2023-06-05 09:07:28,354] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:07:28,358] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:07:28,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference
[2023-06-05 09:07:30,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:07:30,084] [INFO] Task started: Prodigal
[2023-06-05 09:07:30,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg88be5701-61fa-4b6f-a4ed-c0668add84d1/GCA_001304445.1_ASM130444v1_genomic.fna.gz | prodigal -d GCA_001304445.1_ASM130444v1_genomic.fna/cds.fna -a GCA_001304445.1_ASM130444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:07:36,354] [INFO] Task succeeded: Prodigal
[2023-06-05 09:07:36,354] [INFO] Task started: HMMsearch
[2023-06-05 09:07:36,355] [INFO] Running command: hmmsearch --tblout GCA_001304445.1_ASM130444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/reference_markers.hmm GCA_001304445.1_ASM130444v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:07:36,595] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:07:36,597] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88be5701-61fa-4b6f-a4ed-c0668add84d1/GCA_001304445.1_ASM130444v1_genomic.fna.gz]
[2023-06-05 09:07:36,622] [INFO] Query marker FASTA was written to GCA_001304445.1_ASM130444v1_genomic.fna/markers.fasta
[2023-06-05 09:07:36,623] [INFO] Task started: Blastn
[2023-06-05 09:07:36,623] [INFO] Running command: blastn -query GCA_001304445.1_ASM130444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/reference_markers.fasta -out GCA_001304445.1_ASM130444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:07:37,304] [INFO] Task succeeded: Blastn
[2023-06-05 09:07:37,309] [INFO] Selected 29 target genomes.
[2023-06-05 09:07:37,309] [INFO] Target genome list was writen to GCA_001304445.1_ASM130444v1_genomic.fna/target_genomes.txt
[2023-06-05 09:07:37,316] [INFO] Task started: fastANI
[2023-06-05 09:07:37,317] [INFO] Running command: fastANI --query /var/lib/cwl/stg88be5701-61fa-4b6f-a4ed-c0668add84d1/GCA_001304445.1_ASM130444v1_genomic.fna.gz --refList GCA_001304445.1_ASM130444v1_genomic.fna/target_genomes.txt --output GCA_001304445.1_ASM130444v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:07:54,530] [INFO] Task succeeded: fastANI
[2023-06-05 09:07:54,531] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:07:54,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:07:54,540] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:07:54,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:07:54,540] [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
Thiohalophilus thiocyanatoxydans	strain=DSM 16326	GCA_004366735.1	381308	381308	type	True	76.4576	56	709	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.4188	64	709	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2899	63	709	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.2254	51	709	95	below_threshold
Sulfuriflexus mobilis	strain=aks1	GCA_003967195.1	1811807	1811807	type	True	76.1019	52	709	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:07:54,542] [INFO] DFAST Taxonomy check result was written to GCA_001304445.1_ASM130444v1_genomic.fna/tc_result.tsv
[2023-06-05 09:07:54,542] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:07:54,543] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:07:54,543] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/checkm_data
[2023-06-05 09:07:54,544] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:07:54,574] [INFO] Task started: CheckM
[2023-06-05 09:07:54,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001304445.1_ASM130444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001304445.1_ASM130444v1_genomic.fna/checkm_input GCA_001304445.1_ASM130444v1_genomic.fna/checkm_result
[2023-06-05 09:08:19,993] [INFO] Task succeeded: CheckM
[2023-06-05 09:08:19,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 6.94%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-05 09:08:20,017] [INFO] ===== Completeness check finished =====
[2023-06-05 09:08:20,018] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:08:20,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001304445.1_ASM130444v1_genomic.fna/markers.fasta)
[2023-06-05 09:08:20,018] [INFO] Task started: Blastn
[2023-06-05 09:08:20,019] [INFO] Running command: blastn -query GCA_001304445.1_ASM130444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0653f71d-2445-488d-97d7-05a0bdb0e3d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_001304445.1_ASM130444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:08:21,052] [INFO] Task succeeded: Blastn
[2023-06-05 09:08:21,058] [INFO] Selected 29 target genomes.
[2023-06-05 09:08:21,058] [INFO] Target genome list was writen to GCA_001304445.1_ASM130444v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:08:21,279] [INFO] Task started: fastANI
[2023-06-05 09:08:21,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg88be5701-61fa-4b6f-a4ed-c0668add84d1/GCA_001304445.1_ASM130444v1_genomic.fna.gz --refList GCA_001304445.1_ASM130444v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001304445.1_ASM130444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:08:38,922] [INFO] Task succeeded: fastANI
[2023-06-05 09:08:38,933] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 09:08:38,933] [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_004366735.1	s__Thiohalophilus thiocyanatoxydans	76.4576	56	709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__Thiohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355735.1	s__Sulfuricaulis limicola	76.4241	64	709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__Sulfuricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.4097	61	709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840095.1	s__Sulfurivermis sp002840095	76.38	66	709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967195.1	s__Sulfuriflexus mobilis	76.1019	52	709	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__AKS1;f__AKS1;g__Sulfuriflexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:08:38,935] [INFO] GTDB search result was written to GCA_001304445.1_ASM130444v1_genomic.fna/result_gtdb.tsv
[2023-06-05 09:08:38,936] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:08:38,940] [INFO] DFAST_QC result json was written to GCA_001304445.1_ASM130444v1_genomic.fna/dqc_result.json
[2023-06-05 09:08:38,940] [INFO] DFAST_QC completed!
[2023-06-05 09:08:38,940] [INFO] Total running time: 0h1m11s