[2023-03-16 09:23:09,461] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,461] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference
[2023-03-16 09:23:11,228] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:11,229] [INFO] Task started: Prodigal
[2023-03-16 09:23:11,229] [INFO] Running command: cat /var/lib/cwl/stg9f2165ef-92bb-4a9e-aa5d-0c5a218ee843/OceanDNA-b1478.fa | prodigal -d OceanDNA-b1478/cds.fna -a OceanDNA-b1478/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:23:27,221] [INFO] Task succeeded: Prodigal
[2023-03-16 09:23:27,221] [INFO] Task started: HMMsearch
[2023-03-16 09:23:27,221] [INFO] Running command: hmmsearch --tblout OceanDNA-b1478/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/reference_markers.hmm OceanDNA-b1478/protein.faa > /dev/null
[2023-03-16 09:23:27,407] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:23:27,408] [INFO] Found 6/6 markers.
[2023-03-16 09:23:27,430] [INFO] Query marker FASTA was written to OceanDNA-b1478/markers.fasta
[2023-03-16 09:23:27,431] [INFO] Task started: Blastn
[2023-03-16 09:23:27,432] [INFO] Running command: blastn -query OceanDNA-b1478/markers.fasta -db /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/reference_markers.fasta -out OceanDNA-b1478/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:27,935] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:27,937] [INFO] Selected 9 target genomes.
[2023-03-16 09:23:27,938] [INFO] Target genome list was writen to OceanDNA-b1478/target_genomes.txt
[2023-03-16 09:23:27,944] [INFO] Task started: fastANI
[2023-03-16 09:23:27,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f2165ef-92bb-4a9e-aa5d-0c5a218ee843/OceanDNA-b1478.fa --refList OceanDNA-b1478/target_genomes.txt --output OceanDNA-b1478/fastani_result.tsv --threads 1
[2023-03-16 09:23:32,699] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:32,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:23:32,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:23:32,700] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:23:32,700] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:23:32,700] [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
--------------------------------------------------------------------------------
[2023-03-16 09:23:32,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1478/tc_result.tsv
[2023-03-16 09:23:32,703] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:23:32,703] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:23:32,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/checkm_data
[2023-03-16 09:23:32,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:23:32,712] [INFO] Task started: CheckM
[2023-03-16 09:23:32,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1478/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1478/checkm_input OceanDNA-b1478/checkm_result
[2023-03-16 09:24:15,422] [INFO] Task succeeded: CheckM
[2023-03-16 09:24:15,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:24:15,476] [INFO] ===== Completeness check finished =====
[2023-03-16 09:24:15,476] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:24:15,476] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1478/markers.fasta)
[2023-03-16 09:24:15,476] [INFO] Task started: Blastn
[2023-03-16 09:24:15,476] [INFO] Running command: blastn -query OceanDNA-b1478/markers.fasta -db /var/lib/cwl/stg6b9f3b65-4ff9-411a-bd4b-13199d0756ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1478/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:24:16,215] [INFO] Task succeeded: Blastn
[2023-03-16 09:24:16,217] [INFO] Selected 11 target genomes.
[2023-03-16 09:24:16,217] [INFO] Target genome list was writen to OceanDNA-b1478/target_genomes_gtdb.txt
[2023-03-16 09:24:16,238] [INFO] Task started: fastANI
[2023-03-16 09:24:16,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f2165ef-92bb-4a9e-aa5d-0c5a218ee843/OceanDNA-b1478.fa --refList OceanDNA-b1478/target_genomes_gtdb.txt --output OceanDNA-b1478/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:24:22,368] [INFO] Task succeeded: fastANI
[2023-03-16 09:24:22,373] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:24:22,373] [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_014239555.1	s__UBA2110 sp014239555	99.6495	811	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002331465.1	s__UBA2110 sp002331465	90.025	597	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960315.1	s__UBA2110 sp012960315	89.004	761	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002719335.1	s__UBA2110 sp002719335	83.0486	550	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	96.75	96.75	0.83	0.83	2	-
GCA_002388005.1	s__UBA2110 sp002388005	78.5116	371	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705305.1	s__UBA2110 sp002705305	78.2362	349	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__UBA2110	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713975.1	s__MedAcidi-G3 sp002713975	78.0986	70	848	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__TK06;g__MedAcidi-G3	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:24:22,376] [INFO] GTDB search result was written to OceanDNA-b1478/result_gtdb.tsv
[2023-03-16 09:24:22,377] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:24:22,380] [INFO] DFAST_QC result json was written to OceanDNA-b1478/dqc_result.json
[2023-03-16 09:24:22,380] [INFO] DFAST_QC completed!
[2023-03-16 09:24:22,380] [INFO] Total running time: 0h1m13s