[2023-03-15 14:47:21,418] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:47:21,418] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:47:21,418] [INFO] DQC Reference Directory: /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference
[2023-03-15 14:47:22,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:47:22,556] [INFO] Task started: Prodigal
[2023-03-15 14:47:22,556] [INFO] Running command: cat /var/lib/cwl/stgf7c7d360-0427-466d-b83a-abadcadae60d/OceanDNA-b42695.fa | prodigal -d OceanDNA-b42695/cds.fna -a OceanDNA-b42695/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:47:25,918] [INFO] Task succeeded: Prodigal
[2023-03-15 14:47:25,918] [INFO] Task started: HMMsearch
[2023-03-15 14:47:25,918] [INFO] Running command: hmmsearch --tblout OceanDNA-b42695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/reference_markers.hmm OceanDNA-b42695/protein.faa > /dev/null
[2023-03-15 14:47:26,068] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:47:26,069] [INFO] Found 6/6 markers.
[2023-03-15 14:47:26,081] [INFO] Query marker FASTA was written to OceanDNA-b42695/markers.fasta
[2023-03-15 14:47:26,081] [INFO] Task started: Blastn
[2023-03-15 14:47:26,081] [INFO] Running command: blastn -query OceanDNA-b42695/markers.fasta -db /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/reference_markers.fasta -out OceanDNA-b42695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:26,579] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:26,582] [INFO] Selected 10 target genomes.
[2023-03-15 14:47:26,583] [INFO] Target genome list was writen to OceanDNA-b42695/target_genomes.txt
[2023-03-15 14:47:26,589] [INFO] Task started: fastANI
[2023-03-15 14:47:26,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7c7d360-0427-466d-b83a-abadcadae60d/OceanDNA-b42695.fa --refList OceanDNA-b42695/target_genomes.txt --output OceanDNA-b42695/fastani_result.tsv --threads 1
[2023-03-15 14:47:30,288] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:30,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:47:30,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:47:30,289] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:47:30,289] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:47:30,289] [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
--------------------------------------------------------------------------------
[2023-03-15 14:47:30,291] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42695/tc_result.tsv
[2023-03-15 14:47:30,292] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:47:30,292] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:47:30,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/checkm_data
[2023-03-15 14:47:30,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:47:30,331] [INFO] Task started: CheckM
[2023-03-15 14:47:30,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42695/checkm_input OceanDNA-b42695/checkm_result
[2023-03-15 14:47:45,797] [INFO] Task succeeded: CheckM
[2023-03-15 14:47:45,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.52%
Contamintation: 6.48%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 14:47:45,851] [INFO] ===== Completeness check finished =====
[2023-03-15 14:47:45,851] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:47:45,852] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42695/markers.fasta)
[2023-03-15 14:47:45,852] [INFO] Task started: Blastn
[2023-03-15 14:47:45,852] [INFO] Running command: blastn -query OceanDNA-b42695/markers.fasta -db /var/lib/cwl/stge2e054a9-1d5a-43d7-bb2c-5b6b7ee793f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:47:46,550] [INFO] Task succeeded: Blastn
[2023-03-15 14:47:46,554] [INFO] Selected 16 target genomes.
[2023-03-15 14:47:46,554] [INFO] Target genome list was writen to OceanDNA-b42695/target_genomes_gtdb.txt
[2023-03-15 14:47:46,638] [INFO] Task started: fastANI
[2023-03-15 14:47:46,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7c7d360-0427-466d-b83a-abadcadae60d/OceanDNA-b42695.fa --refList OceanDNA-b42695/target_genomes_gtdb.txt --output OceanDNA-b42695/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:47:49,425] [INFO] Task succeeded: fastANI
[2023-03-15 14:47:49,427] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:47:49,428] [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_003331605.1	s__TMED112 sp003331605	93.9142	125	131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779525.1	s__TMED112 sp016779525	89.7804	102	131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	98.73	98.73	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-03-15 14:47:49,429] [INFO] GTDB search result was written to OceanDNA-b42695/result_gtdb.tsv
[2023-03-15 14:47:49,429] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:47:49,430] [INFO] DFAST_QC result json was written to OceanDNA-b42695/dqc_result.json
[2023-03-15 14:47:49,431] [INFO] DFAST_QC completed!
[2023-03-15 14:47:49,431] [INFO] Total running time: 0h0m28s