[2024-01-24 12:31:33,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:33,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:33,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference
[2024-01-24 12:31:35,052] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:35,053] [INFO] Task started: Prodigal
[2024-01-24 12:31:35,053] [INFO] Running command: gunzip -c /var/lib/cwl/stg9be9faf5-e486-43df-a979-fbc0b2e9db0d/GCF_000931935.2_ASM93193v2_genomic.fna.gz | prodigal -d GCF_000931935.2_ASM93193v2_genomic.fna/cds.fna -a GCF_000931935.2_ASM93193v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:51,461] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:51,461] [INFO] Task started: HMMsearch
[2024-01-24 12:31:51,461] [INFO] Running command: hmmsearch --tblout GCF_000931935.2_ASM93193v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/reference_markers.hmm GCF_000931935.2_ASM93193v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:51,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:51,770] [INFO] Found 6/6 markers.
[2024-01-24 12:31:51,823] [INFO] Query marker FASTA was written to GCF_000931935.2_ASM93193v2_genomic.fna/markers.fasta
[2024-01-24 12:31:51,823] [INFO] Task started: Blastn
[2024-01-24 12:31:51,824] [INFO] Running command: blastn -query GCF_000931935.2_ASM93193v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/reference_markers.fasta -out GCF_000931935.2_ASM93193v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:52,442] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:52,446] [INFO] Selected 18 target genomes.
[2024-01-24 12:31:52,447] [INFO] Target genome list was writen to GCF_000931935.2_ASM93193v2_genomic.fna/target_genomes.txt
[2024-01-24 12:31:52,464] [INFO] Task started: fastANI
[2024-01-24 12:31:52,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg9be9faf5-e486-43df-a979-fbc0b2e9db0d/GCF_000931935.2_ASM93193v2_genomic.fna.gz --refList GCF_000931935.2_ASM93193v2_genomic.fna/target_genomes.txt --output GCF_000931935.2_ASM93193v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:06,385] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:06,386] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:06,386] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:06,395] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:06,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:06,396] [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
Dethiosulfatarculus sandiegensis	strain=SPR	GCA_000931935.2	1429043	1429043	type	True	100.0	1934	1938	95	conclusive
Desulfarculus baarsii	strain=DSM 2075	GCA_000143965.1	453230	453230	type	True	76.3314	119	1938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:06,398] [INFO] DFAST Taxonomy check result was written to GCF_000931935.2_ASM93193v2_genomic.fna/tc_result.tsv
[2024-01-24 12:32:06,399] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:06,399] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:06,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/checkm_data
[2024-01-24 12:32:06,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:06,461] [INFO] Task started: CheckM
[2024-01-24 12:32:06,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000931935.2_ASM93193v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000931935.2_ASM93193v2_genomic.fna/checkm_input GCF_000931935.2_ASM93193v2_genomic.fna/checkm_result
[2024-01-24 12:32:55,434] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:55,436] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:55,457] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:55,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:55,458] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000931935.2_ASM93193v2_genomic.fna/markers.fasta)
[2024-01-24 12:32:55,459] [INFO] Task started: Blastn
[2024-01-24 12:32:55,459] [INFO] Running command: blastn -query GCF_000931935.2_ASM93193v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca64f3b-edff-4818-a341-7b8643428d13/dqc_reference/reference_markers_gtdb.fasta -out GCF_000931935.2_ASM93193v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:56,290] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:56,294] [INFO] Selected 21 target genomes.
[2024-01-24 12:32:56,295] [INFO] Target genome list was writen to GCF_000931935.2_ASM93193v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:56,319] [INFO] Task started: fastANI
[2024-01-24 12:32:56,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg9be9faf5-e486-43df-a979-fbc0b2e9db0d/GCF_000931935.2_ASM93193v2_genomic.fna.gz --refList GCF_000931935.2_ASM93193v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000931935.2_ASM93193v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:08,404] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:08,418] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:08,418] [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_000931935.2	s__Dethiosulfatarculus sandiegensis	100.0	1934	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Dethiosulfatarculus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003605055.1	s__SURF-10 sp003605055	76.8311	116	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018902755.1	s__SURF-10 sp018902755	76.8133	154	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.98	99.96	0.97	0.96	6	-
GCA_018896025.1	s__SURF-10 sp018896025	76.7318	148	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.58	98.82	0.97	0.95	4	-
GCF_001184205.1	s__Desulfocarbo indianensis	76.7193	196	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__Desulfocarbo	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002011835.1	s__JdFR-95 sp002011835	76.7134	99	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JdFR-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018819925.1	s__SURF-10 sp018819925	76.6397	139	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__SURF-10	95.0	99.87	99.83	0.95	0.93	4	-
GCA_016218705.1	s__JACRDC01 sp016218705	76.2436	160	1938	d__Bacteria;p__Desulfobacterota;c__Desulfarculia;o__Desulfarculales;f__Desulfarculaceae;g__JACRDC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,420] [INFO] GTDB search result was written to GCF_000931935.2_ASM93193v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:08,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:08,423] [INFO] DFAST_QC result json was written to GCF_000931935.2_ASM93193v2_genomic.fna/dqc_result.json
[2024-01-24 12:33:08,423] [INFO] DFAST_QC completed!
[2024-01-24 12:33:08,423] [INFO] Total running time: 0h1m35s