[2023-03-17 23:08:31,911] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,912] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,912] [INFO] DQC Reference Directory: /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference
[2023-03-17 23:08:33,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,080] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,080] [INFO] Running command: cat /var/lib/cwl/stgcf024a59-4a91-44a4-8d60-da7b70d71a87/OceanDNA-b22965.fa | prodigal -d OceanDNA-b22965/cds.fna -a OceanDNA-b22965/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:09:07,273] [INFO] Task succeeded: Prodigal
[2023-03-17 23:09:07,274] [INFO] Task started: HMMsearch
[2023-03-17 23:09:07,274] [INFO] Running command: hmmsearch --tblout OceanDNA-b22965/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/reference_markers.hmm OceanDNA-b22965/protein.faa > /dev/null
[2023-03-17 23:09:07,550] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:09:07,551] [INFO] Found 6/6 markers.
[2023-03-17 23:09:07,595] [INFO] Query marker FASTA was written to OceanDNA-b22965/markers.fasta
[2023-03-17 23:09:07,596] [INFO] Task started: Blastn
[2023-03-17 23:09:07,596] [INFO] Running command: blastn -query OceanDNA-b22965/markers.fasta -db /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/reference_markers.fasta -out OceanDNA-b22965/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:08,136] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:08,144] [INFO] Selected 23 target genomes.
[2023-03-17 23:09:08,144] [INFO] Target genome list was writen to OceanDNA-b22965/target_genomes.txt
[2023-03-17 23:09:08,158] [INFO] Task started: fastANI
[2023-03-17 23:09:08,158] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf024a59-4a91-44a4-8d60-da7b70d71a87/OceanDNA-b22965.fa --refList OceanDNA-b22965/target_genomes.txt --output OceanDNA-b22965/fastani_result.tsv --threads 1
[2023-03-17 23:09:25,338] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:25,338] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:25,338] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:25,342] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:25,342] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:09:25,342] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.4819	78	1653	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:09:25,344] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22965/tc_result.tsv
[2023-03-17 23:09:25,347] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:25,347] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:25,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/checkm_data
[2023-03-17 23:09:25,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:25,359] [INFO] Task started: CheckM
[2023-03-17 23:09:25,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22965/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22965/checkm_input OceanDNA-b22965/checkm_result
[2023-03-17 23:11:11,603] [INFO] Task succeeded: CheckM
[2023-03-17 23:11:11,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:11:11,625] [INFO] ===== Completeness check finished =====
[2023-03-17 23:11:11,625] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:11:11,626] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22965/markers.fasta)
[2023-03-17 23:11:11,627] [INFO] Task started: Blastn
[2023-03-17 23:11:11,627] [INFO] Running command: blastn -query OceanDNA-b22965/markers.fasta -db /var/lib/cwl/stg248aa842-ae47-4126-9d3a-8d3925f65a8e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22965/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:11:12,346] [INFO] Task succeeded: Blastn
[2023-03-17 23:11:12,353] [INFO] Selected 19 target genomes.
[2023-03-17 23:11:12,354] [INFO] Target genome list was writen to OceanDNA-b22965/target_genomes_gtdb.txt
[2023-03-17 23:11:12,418] [INFO] Task started: fastANI
[2023-03-17 23:11:12,418] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf024a59-4a91-44a4-8d60-da7b70d71a87/OceanDNA-b22965.fa --refList OceanDNA-b22965/target_genomes_gtdb.txt --output OceanDNA-b22965/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:11:30,602] [INFO] Task succeeded: fastANI
[2023-03-17 23:11:30,606] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:11:30,607] [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_002724415.1	s__UBA8437 sp002724415	98.5047	1494	1653	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003445035.1	s__UBA8437 sp003445035	79.5211	874	1653	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	79.3448	868	1653	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_002726205.1	s__GCA-2726205 sp002726205	77.4766	530	1653	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__GCA-2726205	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	75.4941	77	1653	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:11:30,610] [INFO] GTDB search result was written to OceanDNA-b22965/result_gtdb.tsv
[2023-03-17 23:11:30,613] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:11:30,617] [INFO] DFAST_QC result json was written to OceanDNA-b22965/dqc_result.json
[2023-03-17 23:11:30,617] [INFO] DFAST_QC completed!
[2023-03-17 23:11:30,618] [INFO] Total running time: 0h2m59s