[2023-03-15 16:14:47,336] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:14:47,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:14:47,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference
[2023-03-15 16:14:49,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:14:49,239] [INFO] Task started: Prodigal
[2023-03-15 16:14:49,239] [INFO] Running command: cat /var/lib/cwl/stg081a8c9d-2c13-4969-8bbe-4ad1fefea611/OceanDNA-b46766.fa | prodigal -d OceanDNA-b46766/cds.fna -a OceanDNA-b46766/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:21,697] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:21,697] [INFO] Task started: HMMsearch
[2023-03-15 16:15:21,697] [INFO] Running command: hmmsearch --tblout OceanDNA-b46766/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/reference_markers.hmm OceanDNA-b46766/protein.faa > /dev/null
[2023-03-15 16:15:21,920] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:21,921] [INFO] Found 6/6 markers.
[2023-03-15 16:15:21,958] [INFO] Query marker FASTA was written to OceanDNA-b46766/markers.fasta
[2023-03-15 16:15:21,959] [INFO] Task started: Blastn
[2023-03-15 16:15:21,959] [INFO] Running command: blastn -query OceanDNA-b46766/markers.fasta -db /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/reference_markers.fasta -out OceanDNA-b46766/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:22,494] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:22,501] [INFO] Selected 17 target genomes.
[2023-03-15 16:15:22,502] [INFO] Target genome list was writen to OceanDNA-b46766/target_genomes.txt
[2023-03-15 16:15:22,513] [INFO] Task started: fastANI
[2023-03-15 16:15:22,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg081a8c9d-2c13-4969-8bbe-4ad1fefea611/OceanDNA-b46766.fa --refList OceanDNA-b46766/target_genomes.txt --output OceanDNA-b46766/fastani_result.tsv --threads 1
[2023-03-15 16:15:36,505] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:36,506] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:36,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:36,510] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:36,510] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:15:36,510] [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
Roseibacillus persicicus	strain=KCTC 12988	GCA_014651675.1	454148	454148	type	True	76.0764	54	1255	95	below_threshold
Roseibacillus ishigakijimensis	strain=KCTC 12986	GCA_016595415.1	454146	454146	type	True	75.7796	50	1255	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:36,513] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46766/tc_result.tsv
[2023-03-15 16:15:36,517] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:36,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:36,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/checkm_data
[2023-03-15 16:15:36,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:36,527] [INFO] Task started: CheckM
[2023-03-15 16:15:36,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46766/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46766/checkm_input OceanDNA-b46766/checkm_result
[2023-03-15 16:16:57,004] [INFO] Task succeeded: CheckM
[2023-03-15 16:16:57,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:16:57,009] [INFO] ===== Completeness check finished =====
[2023-03-15 16:16:57,009] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:16:57,009] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46766/markers.fasta)
[2023-03-15 16:16:57,011] [INFO] Task started: Blastn
[2023-03-15 16:16:57,011] [INFO] Running command: blastn -query OceanDNA-b46766/markers.fasta -db /var/lib/cwl/stg735d81b6-69c1-41bf-997c-8d75eb6bdcbc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46766/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:16:57,797] [INFO] Task succeeded: Blastn
[2023-03-15 16:16:57,798] [INFO] Selected 23 target genomes.
[2023-03-15 16:16:57,798] [INFO] Target genome list was writen to OceanDNA-b46766/target_genomes_gtdb.txt
[2023-03-15 16:16:58,047] [INFO] Task started: fastANI
[2023-03-15 16:16:58,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg081a8c9d-2c13-4969-8bbe-4ad1fefea611/OceanDNA-b46766.fa --refList OceanDNA-b46766/target_genomes_gtdb.txt --output OceanDNA-b46766/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:17:13,558] [INFO] Task succeeded: fastANI
[2023-03-15 16:17:13,564] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:17:13,565] [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_002323895.1	s__SW10 sp002323895	76.8615	98	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.17	98.66	0.86	0.81	3	-
GCA_002420315.1	s__SW10 sp002420315	76.6316	88	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	97.54	96.31	0.84	0.80	11	-
GCA_018222765.1	s__SW10 sp018222765	76.5849	146	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729295.1	s__SW10 sp002729295	76.5079	106	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	99.31	99.31	0.79	0.79	2	-
GCA_002172625.1	s__SW10 sp002172625	76.4695	130	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	98.72	98.72	0.89	0.89	2	-
GCF_014651675.1	s__Roseibacillus persicicus	76.0764	54	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182405.1	s__SW10 sp905182405	75.9038	105	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__SW10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	75.8296	50	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595415.1	s__Roseibacillus ishigakijimensis	75.7796	50	1255	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:17:13,565] [INFO] GTDB search result was written to OceanDNA-b46766/result_gtdb.tsv
[2023-03-15 16:17:13,565] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:17:13,566] [INFO] DFAST_QC result json was written to OceanDNA-b46766/dqc_result.json
[2023-03-15 16:17:13,566] [INFO] DFAST_QC completed!
[2023-03-15 16:17:13,566] [INFO] Total running time: 0h2m26s