[2023-06-28 06:25:40,987] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:25:40,988] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:25:40,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference
[2023-06-28 06:25:42,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:25:42,295] [INFO] Task started: Prodigal
[2023-06-28 06:25:42,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fce0613-9a47-4365-961b-9e3f48ed05f9/GCA_017989485.1_ASM1798948v1_genomic.fna.gz | prodigal -d GCA_017989485.1_ASM1798948v1_genomic.fna/cds.fna -a GCA_017989485.1_ASM1798948v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:25:47,798] [INFO] Task succeeded: Prodigal
[2023-06-28 06:25:47,799] [INFO] Task started: HMMsearch
[2023-06-28 06:25:47,799] [INFO] Running command: hmmsearch --tblout GCA_017989485.1_ASM1798948v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/reference_markers.hmm GCA_017989485.1_ASM1798948v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:25:47,996] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:25:47,998] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9fce0613-9a47-4365-961b-9e3f48ed05f9/GCA_017989485.1_ASM1798948v1_genomic.fna.gz]
[2023-06-28 06:25:48,027] [INFO] Query marker FASTA was written to GCA_017989485.1_ASM1798948v1_genomic.fna/markers.fasta
[2023-06-28 06:25:48,027] [INFO] Task started: Blastn
[2023-06-28 06:25:48,027] [INFO] Running command: blastn -query GCA_017989485.1_ASM1798948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/reference_markers.fasta -out GCA_017989485.1_ASM1798948v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:25:48,644] [INFO] Task succeeded: Blastn
[2023-06-28 06:25:48,648] [INFO] Selected 25 target genomes.
[2023-06-28 06:25:48,648] [INFO] Target genome list was writen to GCA_017989485.1_ASM1798948v1_genomic.fna/target_genomes.txt
[2023-06-28 06:25:48,660] [INFO] Task started: fastANI
[2023-06-28 06:25:48,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fce0613-9a47-4365-961b-9e3f48ed05f9/GCA_017989485.1_ASM1798948v1_genomic.fna.gz --refList GCA_017989485.1_ASM1798948v1_genomic.fna/target_genomes.txt --output GCA_017989485.1_ASM1798948v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:26:01,559] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:01,560] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:26:01,560] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:26:01,566] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:26:01,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:26:01,567] [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
Vitreoscilla massiliensis	strain=SN6	GCA_001457815.1	1689272	1689272	type	True	76.5056	70	528	95	below_threshold
Vitreoscilla massiliensis	strain=SN4	GCA_022870925.1	1689272	1689272	type	True	76.3993	71	528	95	below_threshold
Uruburuella testudinis	strain=CCUG 63373m	GCA_022870865.1	1282863	1282863	type	True	76.2228	55	528	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:26:01,569] [INFO] DFAST Taxonomy check result was written to GCA_017989485.1_ASM1798948v1_genomic.fna/tc_result.tsv
[2023-06-28 06:26:01,571] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:26:01,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:26:01,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/checkm_data
[2023-06-28 06:26:01,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:26:01,601] [INFO] Task started: CheckM
[2023-06-28 06:26:01,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017989485.1_ASM1798948v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017989485.1_ASM1798948v1_genomic.fna/checkm_input GCA_017989485.1_ASM1798948v1_genomic.fna/checkm_result
[2023-06-28 06:26:25,382] [INFO] Task succeeded: CheckM
[2023-06-28 06:26:25,383] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:26:25,405] [INFO] ===== Completeness check finished =====
[2023-06-28 06:26:25,405] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:26:25,405] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017989485.1_ASM1798948v1_genomic.fna/markers.fasta)
[2023-06-28 06:26:25,406] [INFO] Task started: Blastn
[2023-06-28 06:26:25,406] [INFO] Running command: blastn -query GCA_017989485.1_ASM1798948v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ffb0ca3-6048-413a-bb01-29d4ca593700/dqc_reference/reference_markers_gtdb.fasta -out GCA_017989485.1_ASM1798948v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:26:26,229] [INFO] Task succeeded: Blastn
[2023-06-28 06:26:26,236] [INFO] Selected 14 target genomes.
[2023-06-28 06:26:26,236] [INFO] Target genome list was writen to GCA_017989485.1_ASM1798948v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:26:26,247] [INFO] Task started: fastANI
[2023-06-28 06:26:26,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fce0613-9a47-4365-961b-9e3f48ed05f9/GCA_017989485.1_ASM1798948v1_genomic.fna.gz --refList GCA_017989485.1_ASM1798948v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017989485.1_ASM1798948v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:26:33,402] [INFO] Task succeeded: fastANI
[2023-06-28 06:26:33,412] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:26:33,412] [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_017989485.1	s__JAGNPU01 sp017989485	100.0	519	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017991555.1	s__JAGNPU01 sp017991555	82.9079	402	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	99.61	99.61	0.99	0.99	2	-
GCA_017987415.1	s__JAGNPU01 sp017987415	82.6484	334	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__JAGNPU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457815.1	s__Vitreoscilla massiliensis	76.5056	70	528	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Neisseriaceae;g__Vitreoscilla	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 06:26:33,414] [INFO] GTDB search result was written to GCA_017989485.1_ASM1798948v1_genomic.fna/result_gtdb.tsv
[2023-06-28 06:26:33,415] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:26:33,418] [INFO] DFAST_QC result json was written to GCA_017989485.1_ASM1798948v1_genomic.fna/dqc_result.json
[2023-06-28 06:26:33,418] [INFO] DFAST_QC completed!
[2023-06-28 06:26:33,418] [INFO] Total running time: 0h0m52s