[2023-03-18 07:29:30,337] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,337] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference
[2023-03-18 07:29:31,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stgc6e2be68-4888-469e-9e30-dffc41a031eb/OceanDNA-b11191.fa | prodigal -d OceanDNA-b11191/cds.fna -a OceanDNA-b11191/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:43,902] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:43,902] [INFO] Task started: HMMsearch
[2023-03-18 07:29:43,902] [INFO] Running command: hmmsearch --tblout OceanDNA-b11191/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/reference_markers.hmm OceanDNA-b11191/protein.faa > /dev/null
[2023-03-18 07:29:44,086] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:44,087] [INFO] Found 6/6 markers.
[2023-03-18 07:29:44,099] [INFO] Query marker FASTA was written to OceanDNA-b11191/markers.fasta
[2023-03-18 07:29:44,099] [INFO] Task started: Blastn
[2023-03-18 07:29:44,099] [INFO] Running command: blastn -query OceanDNA-b11191/markers.fasta -db /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/reference_markers.fasta -out OceanDNA-b11191/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:44,623] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:44,624] [INFO] Selected 23 target genomes.
[2023-03-18 07:29:44,624] [INFO] Target genome list was writen to OceanDNA-b11191/target_genomes.txt
[2023-03-18 07:29:44,635] [INFO] Task started: fastANI
[2023-03-18 07:29:44,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e2be68-4888-469e-9e30-dffc41a031eb/OceanDNA-b11191.fa --refList OceanDNA-b11191/target_genomes.txt --output OceanDNA-b11191/fastani_result.tsv --threads 1
[2023-03-18 07:29:57,571] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:57,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:57,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:57,572] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:57,572] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:57,572] [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
--------------------------------------------------------------------------------
[2023-03-18 07:29:57,572] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11191/tc_result.tsv
[2023-03-18 07:29:57,572] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:57,572] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:57,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/checkm_data
[2023-03-18 07:29:57,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:57,578] [INFO] Task started: CheckM
[2023-03-18 07:29:57,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11191/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11191/checkm_input OceanDNA-b11191/checkm_result
[2023-03-18 07:30:31,591] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:31,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:31,594] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:31,594] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:31,594] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11191/markers.fasta)
[2023-03-18 07:30:31,594] [INFO] Task started: Blastn
[2023-03-18 07:30:31,594] [INFO] Running command: blastn -query OceanDNA-b11191/markers.fasta -db /var/lib/cwl/stg9f52aaa2-c739-4802-90ab-8414d79c638b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11191/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:32,294] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:32,295] [INFO] Selected 12 target genomes.
[2023-03-18 07:30:32,295] [INFO] Target genome list was writen to OceanDNA-b11191/target_genomes_gtdb.txt
[2023-03-18 07:30:32,538] [INFO] Task started: fastANI
[2023-03-18 07:30:32,538] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6e2be68-4888-469e-9e30-dffc41a031eb/OceanDNA-b11191.fa --refList OceanDNA-b11191/target_genomes_gtdb.txt --output OceanDNA-b11191/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:37,191] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:37,197] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:30:37,197] [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_002364535.1	s__UBA8316 sp002364535	82.5209	383	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018623955.1	s__UBA8316 sp018623955	81.0145	184	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	80.1971	276	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002687665.1	s__UBA8316 sp002687665	79.8188	215	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390455.1	s__UBA8316 sp002390455	79.7656	308	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_902619315.1	s__UBA8316 sp902619315	79.2378	227	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336305.1	s__UBA8316 sp002336305	79.1529	267	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	78.2118	195	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003538555.1	s__UBA8316 sp003538555	76.8388	70	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:37,198] [INFO] GTDB search result was written to OceanDNA-b11191/result_gtdb.tsv
[2023-03-18 07:30:37,198] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:37,199] [INFO] DFAST_QC result json was written to OceanDNA-b11191/dqc_result.json
[2023-03-18 07:30:37,199] [INFO] DFAST_QC completed!
[2023-03-18 07:30:37,199] [INFO] Total running time: 0h1m7s