[2023-03-18 03:45:10,278] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,278] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference
[2023-03-18 03:45:12,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,149] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,149] [INFO] Running command: cat /var/lib/cwl/stgc6cab08a-2b89-4c77-8dbd-181ce66085da/OceanDNA-b24211.fa | prodigal -d OceanDNA-b24211/cds.fna -a OceanDNA-b24211/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:18,311] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:18,311] [INFO] Task started: HMMsearch
[2023-03-18 03:45:18,311] [INFO] Running command: hmmsearch --tblout OceanDNA-b24211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/reference_markers.hmm OceanDNA-b24211/protein.faa > /dev/null
[2023-03-18 03:45:18,474] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:18,475] [INFO] Found 6/6 markers.
[2023-03-18 03:45:18,483] [INFO] Query marker FASTA was written to OceanDNA-b24211/markers.fasta
[2023-03-18 03:45:18,483] [INFO] Task started: Blastn
[2023-03-18 03:45:18,483] [INFO] Running command: blastn -query OceanDNA-b24211/markers.fasta -db /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/reference_markers.fasta -out OceanDNA-b24211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:19,013] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:19,014] [INFO] Selected 16 target genomes.
[2023-03-18 03:45:19,014] [INFO] Target genome list was writen to OceanDNA-b24211/target_genomes.txt
[2023-03-18 03:45:19,023] [INFO] Task started: fastANI
[2023-03-18 03:45:19,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cab08a-2b89-4c77-8dbd-181ce66085da/OceanDNA-b24211.fa --refList OceanDNA-b24211/target_genomes.txt --output OceanDNA-b24211/fastani_result.tsv --threads 1
[2023-03-18 03:45:25,755] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:25,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:25,755] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:25,758] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:25,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:25,758] [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
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	74.5893	61	365	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:25,759] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24211/tc_result.tsv
[2023-03-18 03:45:25,759] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:25,759] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:25,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/checkm_data
[2023-03-18 03:45:25,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:25,762] [INFO] Task started: CheckM
[2023-03-18 03:45:25,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24211/checkm_input OceanDNA-b24211/checkm_result
[2023-03-18 03:45:46,853] [INFO] Task succeeded: CheckM
[2023-03-18 03:45:46,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:45:46,855] [INFO] ===== Completeness check finished =====
[2023-03-18 03:45:46,855] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:45:46,855] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24211/markers.fasta)
[2023-03-18 03:45:46,855] [INFO] Task started: Blastn
[2023-03-18 03:45:46,855] [INFO] Running command: blastn -query OceanDNA-b24211/markers.fasta -db /var/lib/cwl/stgc26567df-1221-4954-8ef2-d076deabb35b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:47,616] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:47,617] [INFO] Selected 15 target genomes.
[2023-03-18 03:45:47,617] [INFO] Target genome list was writen to OceanDNA-b24211/target_genomes_gtdb.txt
[2023-03-18 03:45:47,686] [INFO] Task started: fastANI
[2023-03-18 03:45:47,687] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cab08a-2b89-4c77-8dbd-181ce66085da/OceanDNA-b24211.fa --refList OceanDNA-b24211/target_genomes_gtdb.txt --output OceanDNA-b24211/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:45:51,070] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:51,075] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:45:51,075] [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_002717245.1	s__GCA-002720895 sp002717245	99.3462	330	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.29	99.29	0.96	0.96	2	conclusive
GCA_902607475.1	s__GCA-002720895 sp902607475	81.4361	195	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937775.1	s__GCA-002720895 sp002937775	81.0012	203	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	99.14	99.14	0.75	0.75	2	-
GCA_002711715.1	s__GCA-002720895 sp002711715	80.5938	124	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720895.1	s__GCA-002720895 sp002720895	80.3581	162	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__GCA-002720895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937815.1	s__PTKQ01 sp002937815	77.4887	73	365	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-002720895;f__GCA-002720895;g__PTKQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:45:51,075] [INFO] GTDB search result was written to OceanDNA-b24211/result_gtdb.tsv
[2023-03-18 03:45:51,075] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:45:51,076] [INFO] DFAST_QC result json was written to OceanDNA-b24211/dqc_result.json
[2023-03-18 03:45:51,076] [INFO] DFAST_QC completed!
[2023-03-18 03:45:51,076] [INFO] Total running time: 0h0m41s