[2023-06-29 19:25:08,897] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:25:08,899] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:25:08,899] [INFO] DQC Reference Directory: /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference
[2023-06-29 19:25:10,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:25:10,446] [INFO] Task started: Prodigal
[2023-06-29 19:25:10,446] [INFO] Running command: gunzip -c /var/lib/cwl/stg26df4262-e112-4d27-83f6-95fc1b53f4f9/GCA_021776475.1_ASM2177647v1_genomic.fna.gz | prodigal -d GCA_021776475.1_ASM2177647v1_genomic.fna/cds.fna -a GCA_021776475.1_ASM2177647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:25:20,915] [INFO] Task succeeded: Prodigal
[2023-06-29 19:25:20,915] [INFO] Task started: HMMsearch
[2023-06-29 19:25:20,915] [INFO] Running command: hmmsearch --tblout GCA_021776475.1_ASM2177647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/reference_markers.hmm GCA_021776475.1_ASM2177647v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:25:21,234] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:25:21,236] [INFO] Found 6/6 markers.
[2023-06-29 19:25:21,265] [INFO] Query marker FASTA was written to GCA_021776475.1_ASM2177647v1_genomic.fna/markers.fasta
[2023-06-29 19:25:21,266] [INFO] Task started: Blastn
[2023-06-29 19:25:21,266] [INFO] Running command: blastn -query GCA_021776475.1_ASM2177647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/reference_markers.fasta -out GCA_021776475.1_ASM2177647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:25:21,979] [INFO] Task succeeded: Blastn
[2023-06-29 19:25:21,982] [INFO] Selected 20 target genomes.
[2023-06-29 19:25:21,983] [INFO] Target genome list was writen to GCA_021776475.1_ASM2177647v1_genomic.fna/target_genomes.txt
[2023-06-29 19:25:21,985] [INFO] Task started: fastANI
[2023-06-29 19:25:21,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg26df4262-e112-4d27-83f6-95fc1b53f4f9/GCA_021776475.1_ASM2177647v1_genomic.fna.gz --refList GCA_021776475.1_ASM2177647v1_genomic.fna/target_genomes.txt --output GCA_021776475.1_ASM2177647v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:25:31,558] [INFO] Task succeeded: fastANI
[2023-06-29 19:25:31,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:25:31,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:25:31,567] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:25:31,568] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:25:31,568] [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
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	76.1781	50	1133	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	75.9583	72	1133	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	75.9371	73	1133	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	75.8952	72	1133	95	below_threshold
Aquisalinus luteolus	strain=NH6-79	GCA_009712425.2	1566827	1566827	type	True	75.6793	63	1133	95	below_threshold
Aquisalinus luteolus	strain=CGMCC 1.14984	GCA_014640455.1	1566827	1566827	type	True	75.6611	64	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:25:31,570] [INFO] DFAST Taxonomy check result was written to GCA_021776475.1_ASM2177647v1_genomic.fna/tc_result.tsv
[2023-06-29 19:25:31,571] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:25:31,572] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:25:31,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/checkm_data
[2023-06-29 19:25:31,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:25:31,615] [INFO] Task started: CheckM
[2023-06-29 19:25:31,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021776475.1_ASM2177647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021776475.1_ASM2177647v1_genomic.fna/checkm_input GCA_021776475.1_ASM2177647v1_genomic.fna/checkm_result
[2023-06-29 19:26:09,721] [INFO] Task succeeded: CheckM
[2023-06-29 19:26:09,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:26:09,747] [INFO] ===== Completeness check finished =====
[2023-06-29 19:26:09,747] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:26:09,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021776475.1_ASM2177647v1_genomic.fna/markers.fasta)
[2023-06-29 19:26:09,748] [INFO] Task started: Blastn
[2023-06-29 19:26:09,748] [INFO] Running command: blastn -query GCA_021776475.1_ASM2177647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga170bad0-64a4-4cc6-85b0-f697393f5233/dqc_reference/reference_markers_gtdb.fasta -out GCA_021776475.1_ASM2177647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:26:10,837] [INFO] Task succeeded: Blastn
[2023-06-29 19:26:10,842] [INFO] Selected 31 target genomes.
[2023-06-29 19:26:10,842] [INFO] Target genome list was writen to GCA_021776475.1_ASM2177647v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:26:10,881] [INFO] Task started: fastANI
[2023-06-29 19:26:10,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg26df4262-e112-4d27-83f6-95fc1b53f4f9/GCA_021776475.1_ASM2177647v1_genomic.fna.gz --refList GCA_021776475.1_ASM2177647v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021776475.1_ASM2177647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:26:27,994] [INFO] Task succeeded: fastANI
[2023-06-29 19:26:28,003] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:26:28,004] [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_002943565.1	s__Marinicaulis flavus	76.1781	50	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	75.9583	72	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001657385.1	s__Marinicaulis sp001657385	75.8674	51	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009712425.2	s__Aquisalinus luteolus	75.6793	63	1133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:26:28,007] [INFO] GTDB search result was written to GCA_021776475.1_ASM2177647v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:26:28,007] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:26:28,011] [INFO] DFAST_QC result json was written to GCA_021776475.1_ASM2177647v1_genomic.fna/dqc_result.json
[2023-06-29 19:26:28,011] [INFO] DFAST_QC completed!
[2023-06-29 19:26:28,011] [INFO] Total running time: 0h1m19s