[2023-03-14 12:33:23,775] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:33:23,775] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:33:23,775] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference
[2023-03-14 12:33:24,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:33:24,932] [INFO] Task started: Prodigal
[2023-03-14 12:33:24,932] [INFO] Running command: cat /var/lib/cwl/stga9d1d014-2a8e-4923-bdbe-0df915bcbab4/OceanDNA-b38426.fa | prodigal -d OceanDNA-b38426/cds.fna -a OceanDNA-b38426/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:33:32,489] [INFO] Task succeeded: Prodigal
[2023-03-14 12:33:32,490] [INFO] Task started: HMMsearch
[2023-03-14 12:33:32,490] [INFO] Running command: hmmsearch --tblout OceanDNA-b38426/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/reference_markers.hmm OceanDNA-b38426/protein.faa > /dev/null
[2023-03-14 12:33:32,649] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:33:32,649] [INFO] Found 6/6 markers.
[2023-03-14 12:33:32,661] [INFO] Query marker FASTA was written to OceanDNA-b38426/markers.fasta
[2023-03-14 12:33:32,663] [INFO] Task started: Blastn
[2023-03-14 12:33:32,663] [INFO] Running command: blastn -query OceanDNA-b38426/markers.fasta -db /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/reference_markers.fasta -out OceanDNA-b38426/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:33:33,191] [INFO] Task succeeded: Blastn
[2023-03-14 12:33:33,192] [INFO] Selected 26 target genomes.
[2023-03-14 12:33:33,192] [INFO] Target genome list was writen to OceanDNA-b38426/target_genomes.txt
[2023-03-14 12:33:33,207] [INFO] Task started: fastANI
[2023-03-14 12:33:33,207] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d1d014-2a8e-4923-bdbe-0df915bcbab4/OceanDNA-b38426.fa --refList OceanDNA-b38426/target_genomes.txt --output OceanDNA-b38426/fastani_result.tsv --threads 1
[2023-03-14 12:33:46,390] [INFO] Task succeeded: fastANI
[2023-03-14 12:33:46,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:33:46,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:33:46,391] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:33:46,391] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:33:46,391] [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
--------------------------------------------------------------------------------
[2023-03-14 12:33:46,392] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38426/tc_result.tsv
[2023-03-14 12:33:46,392] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:33:46,392] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:33:46,392] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/checkm_data
[2023-03-14 12:33:46,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:33:46,399] [INFO] Task started: CheckM
[2023-03-14 12:33:46,399] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38426/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38426/checkm_input OceanDNA-b38426/checkm_result
[2023-03-14 12:34:10,516] [INFO] Task succeeded: CheckM
[2023-03-14 12:34:10,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:34:10,520] [INFO] ===== Completeness check finished =====
[2023-03-14 12:34:10,520] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:34:10,520] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38426/markers.fasta)
[2023-03-14 12:34:10,521] [INFO] Task started: Blastn
[2023-03-14 12:34:10,522] [INFO] Running command: blastn -query OceanDNA-b38426/markers.fasta -db /var/lib/cwl/stg4b172914-e369-46c3-bdaf-fae60988cf91/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38426/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:34:11,227] [INFO] Task succeeded: Blastn
[2023-03-14 12:34:11,230] [INFO] Selected 19 target genomes.
[2023-03-14 12:34:11,230] [INFO] Target genome list was writen to OceanDNA-b38426/target_genomes_gtdb.txt
[2023-03-14 12:34:11,240] [INFO] Task started: fastANI
[2023-03-14 12:34:11,240] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d1d014-2a8e-4923-bdbe-0df915bcbab4/OceanDNA-b38426.fa --refList OceanDNA-b38426/target_genomes_gtdb.txt --output OceanDNA-b38426/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:34:18,922] [INFO] Task succeeded: fastANI
[2023-03-14 12:34:18,927] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:34:18,927] [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_002714245.1	s__HIMB30 sp002714245	92.3037	315	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.14	95.91	0.72	0.71	3	-
GCA_002717305.1	s__HIMB30 sp002717305	85.3123	200	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.98	98.98	0.61	0.61	2	-
GCA_002731015.1	s__HIMB30 sp002731015	85.1214	248	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	99.59	99.59	0.71	0.71	2	-
GCA_002730235.1	s__HIMB30 sp002730235	83.9802	295	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008087055.1	s__HIMB30 sp008087055	77.738	67	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024125.1	s__HIMB30 sp010024125	77.6652	60	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.50	98.43	0.79	0.78	4	-
GCA_009886945.1	s__HIMB30 sp002691485	77.3705	58	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.88	95.73	0.81	0.62	14	-
--------------------------------------------------------------------------------
[2023-03-14 12:34:18,928] [INFO] GTDB search result was written to OceanDNA-b38426/result_gtdb.tsv
[2023-03-14 12:34:18,928] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:34:18,930] [INFO] DFAST_QC result json was written to OceanDNA-b38426/dqc_result.json
[2023-03-14 12:34:18,930] [INFO] DFAST_QC completed!
[2023-03-14 12:34:18,930] [INFO] Total running time: 0h0m55s