[2023-06-13 22:41:47,113] [INFO] DFAST_QC pipeline started.
[2023-06-13 22:41:47,116] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 22:41:47,117] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference
[2023-06-13 22:41:48,320] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 22:41:48,321] [INFO] Task started: Prodigal
[2023-06-13 22:41:48,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg88d6993d-d70f-46c2-a644-76c6f3080ac6/GCA_022759005.1_ASM2275900v1_genomic.fna.gz | prodigal -d GCA_022759005.1_ASM2275900v1_genomic.fna/cds.fna -a GCA_022759005.1_ASM2275900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 22:41:52,435] [INFO] Task succeeded: Prodigal
[2023-06-13 22:41:52,436] [INFO] Task started: HMMsearch
[2023-06-13 22:41:52,436] [INFO] Running command: hmmsearch --tblout GCA_022759005.1_ASM2275900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/reference_markers.hmm GCA_022759005.1_ASM2275900v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 22:41:52,680] [INFO] Task succeeded: HMMsearch
[2023-06-13 22:41:52,682] [INFO] Found 6/6 markers.
[2023-06-13 22:41:52,710] [INFO] Query marker FASTA was written to GCA_022759005.1_ASM2275900v1_genomic.fna/markers.fasta
[2023-06-13 22:41:52,710] [INFO] Task started: Blastn
[2023-06-13 22:41:52,711] [INFO] Running command: blastn -query GCA_022759005.1_ASM2275900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/reference_markers.fasta -out GCA_022759005.1_ASM2275900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:41:53,285] [INFO] Task succeeded: Blastn
[2023-06-13 22:41:53,290] [INFO] Selected 17 target genomes.
[2023-06-13 22:41:53,290] [INFO] Target genome list was writen to GCA_022759005.1_ASM2275900v1_genomic.fna/target_genomes.txt
[2023-06-13 22:41:53,293] [INFO] Task started: fastANI
[2023-06-13 22:41:53,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg88d6993d-d70f-46c2-a644-76c6f3080ac6/GCA_022759005.1_ASM2275900v1_genomic.fna.gz --refList GCA_022759005.1_ASM2275900v1_genomic.fna/target_genomes.txt --output GCA_022759005.1_ASM2275900v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 22:42:00,937] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:00,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 22:42:00,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 22:42:00,951] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 22:42:00,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 22:42:00,951] [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
Sulfuricurvum kujiense	strain=DSM 16994	GCA_000183725.1	148813	148813	type	True	80.5343	338	512	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 22:42:00,954] [INFO] DFAST Taxonomy check result was written to GCA_022759005.1_ASM2275900v1_genomic.fna/tc_result.tsv
[2023-06-13 22:42:00,955] [INFO] ===== Taxonomy check completed =====
[2023-06-13 22:42:00,955] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 22:42:00,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/checkm_data
[2023-06-13 22:42:00,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 22:42:00,983] [INFO] Task started: CheckM
[2023-06-13 22:42:00,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022759005.1_ASM2275900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022759005.1_ASM2275900v1_genomic.fna/checkm_input GCA_022759005.1_ASM2275900v1_genomic.fna/checkm_result
[2023-06-13 22:42:21,211] [INFO] Task succeeded: CheckM
[2023-06-13 22:42:21,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 22:42:21,240] [INFO] ===== Completeness check finished =====
[2023-06-13 22:42:21,240] [INFO] ===== Start GTDB Search =====
[2023-06-13 22:42:21,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022759005.1_ASM2275900v1_genomic.fna/markers.fasta)
[2023-06-13 22:42:21,241] [INFO] Task started: Blastn
[2023-06-13 22:42:21,241] [INFO] Running command: blastn -query GCA_022759005.1_ASM2275900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2c5fc0d-54b8-4572-9ba9-f538d8a36508/dqc_reference/reference_markers_gtdb.fasta -out GCA_022759005.1_ASM2275900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 22:42:22,064] [INFO] Task succeeded: Blastn
[2023-06-13 22:42:22,068] [INFO] Selected 7 target genomes.
[2023-06-13 22:42:22,068] [INFO] Target genome list was writen to GCA_022759005.1_ASM2275900v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 22:42:22,069] [INFO] Task started: fastANI
[2023-06-13 22:42:22,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg88d6993d-d70f-46c2-a644-76c6f3080ac6/GCA_022759005.1_ASM2275900v1_genomic.fna.gz --refList GCA_022759005.1_ASM2275900v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022759005.1_ASM2275900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 22:42:25,019] [INFO] Task succeeded: fastANI
[2023-06-13 22:42:25,031] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 22:42:25,032] [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_002633015.1	s__Sulfuricurvum sp002633015	82.8126	373	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163035.1	s__Sulfuricurvum sp019163035	81.1048	314	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183725.1	s__Sulfuricurvum kujiense	80.5329	339	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002742695.1	s__Sulfuricurvum kujiense_A	80.3682	272	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.70	99.66	0.87	0.87	4	-
GCA_000310245.1	s__Sulfuricurvum sp000310245	80.1629	315	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.06	98.44	0.95	0.92	4	-
GCA_014764105.1	s__Sulfuricurvum sp014764105	79.8514	219	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.42	99.42	0.84	0.84	2	-
GCA_014764075.1	s__Sulfuricurvum sp014764075	79.818	220	512	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 22:42:25,034] [INFO] GTDB search result was written to GCA_022759005.1_ASM2275900v1_genomic.fna/result_gtdb.tsv
[2023-06-13 22:42:25,035] [INFO] ===== GTDB Search completed =====
[2023-06-13 22:42:25,038] [INFO] DFAST_QC result json was written to GCA_022759005.1_ASM2275900v1_genomic.fna/dqc_result.json
[2023-06-13 22:42:25,038] [INFO] DFAST_QC completed!
[2023-06-13 22:42:25,038] [INFO] Total running time: 0h0m38s