[2023-06-05 07:09:45,476] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:45,479] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:45,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference
[2023-06-05 07:09:47,094] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:47,096] [INFO] Task started: Prodigal
[2023-06-05 07:09:47,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d272bc4-27c2-4a0b-9186-b0385be41133/GCA_001830745.1_ASM183074v1_genomic.fna.gz | prodigal -d GCA_001830745.1_ASM183074v1_genomic.fna/cds.fna -a GCA_001830745.1_ASM183074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:51,741] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:51,741] [INFO] Task started: HMMsearch
[2023-06-05 07:09:51,742] [INFO] Running command: hmmsearch --tblout GCA_001830745.1_ASM183074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/reference_markers.hmm GCA_001830745.1_ASM183074v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:52,014] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:52,015] [INFO] Found 6/6 markers.
[2023-06-05 07:09:52,046] [INFO] Query marker FASTA was written to GCA_001830745.1_ASM183074v1_genomic.fna/markers.fasta
[2023-06-05 07:09:52,046] [INFO] Task started: Blastn
[2023-06-05 07:09:52,047] [INFO] Running command: blastn -query GCA_001830745.1_ASM183074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/reference_markers.fasta -out GCA_001830745.1_ASM183074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:52,647] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:52,652] [INFO] Selected 20 target genomes.
[2023-06-05 07:09:52,653] [INFO] Target genome list was writen to GCA_001830745.1_ASM183074v1_genomic.fna/target_genomes.txt
[2023-06-05 07:09:52,659] [INFO] Task started: fastANI
[2023-06-05 07:09:52,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d272bc4-27c2-4a0b-9186-b0385be41133/GCA_001830745.1_ASM183074v1_genomic.fna.gz --refList GCA_001830745.1_ASM183074v1_genomic.fna/target_genomes.txt --output GCA_001830745.1_ASM183074v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:10:04,149] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:04,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:10:04,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:10:04,154] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:10:04,154] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:10:04,154] [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	81.4544	326	504	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:10:04,156] [INFO] DFAST Taxonomy check result was written to GCA_001830745.1_ASM183074v1_genomic.fna/tc_result.tsv
[2023-06-05 07:10:04,157] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:10:04,157] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:10:04,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/checkm_data
[2023-06-05 07:10:04,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:10:04,189] [INFO] Task started: CheckM
[2023-06-05 07:10:04,189] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001830745.1_ASM183074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001830745.1_ASM183074v1_genomic.fna/checkm_input GCA_001830745.1_ASM183074v1_genomic.fna/checkm_result
[2023-06-05 07:10:26,577] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:26,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:10:26,596] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:26,597] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:26,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001830745.1_ASM183074v1_genomic.fna/markers.fasta)
[2023-06-05 07:10:26,598] [INFO] Task started: Blastn
[2023-06-05 07:10:26,598] [INFO] Running command: blastn -query GCA_001830745.1_ASM183074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7930b163-d933-482f-b636-5dc8ef5c383f/dqc_reference/reference_markers_gtdb.fasta -out GCA_001830745.1_ASM183074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:27,443] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:27,455] [INFO] Selected 7 target genomes.
[2023-06-05 07:10:27,455] [INFO] Target genome list was writen to GCA_001830745.1_ASM183074v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:27,456] [INFO] Task started: fastANI
[2023-06-05 07:10:27,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d272bc4-27c2-4a0b-9186-b0385be41133/GCA_001830745.1_ASM183074v1_genomic.fna.gz --refList GCA_001830745.1_ASM183074v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001830745.1_ASM183074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:10:30,523] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:30,534] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:10:30,534] [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_002742695.1	s__Sulfuricurvum kujiense_A	99.6766	438	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.70	99.66	0.87	0.87	4	conclusive
GCA_019163035.1	s__Sulfuricurvum sp019163035	82.8401	292	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000310245.1	s__Sulfuricurvum sp000310245	82.427	327	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.06	98.44	0.95	0.92	4	-
GCF_000183725.1	s__Sulfuricurvum kujiense	81.4544	326	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002633015.1	s__Sulfuricurvum sp002633015	80.515	267	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014764075.1	s__Sulfuricurvum sp014764075	80.2177	176	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000747095.1	s__Sulfuricurvum sp000747095	78.8974	203	504	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurimonadaceae;g__Sulfuricurvum	95.0	99.87	99.87	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-05 07:10:30,537] [INFO] GTDB search result was written to GCA_001830745.1_ASM183074v1_genomic.fna/result_gtdb.tsv
[2023-06-05 07:10:30,538] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:10:30,540] [INFO] DFAST_QC result json was written to GCA_001830745.1_ASM183074v1_genomic.fna/dqc_result.json
[2023-06-05 07:10:30,540] [INFO] DFAST_QC completed!
[2023-06-05 07:10:30,541] [INFO] Total running time: 0h0m45s