[2023-03-17 02:49:37,493] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,493] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,493] [INFO] DQC Reference Directory: /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference
[2023-03-17 02:49:38,733] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,734] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,734] [INFO] Running command: cat /var/lib/cwl/stg29e376c6-6ca5-44ea-8dea-4634e0223e45/OceanDNA-b40594.fa | prodigal -d OceanDNA-b40594/cds.fna -a OceanDNA-b40594/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:49:43,398] [INFO] Task succeeded: Prodigal
[2023-03-17 02:49:43,398] [INFO] Task started: HMMsearch
[2023-03-17 02:49:43,398] [INFO] Running command: hmmsearch --tblout OceanDNA-b40594/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/reference_markers.hmm OceanDNA-b40594/protein.faa > /dev/null
[2023-03-17 02:49:43,543] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:49:43,543] [INFO] Found 6/6 markers.
[2023-03-17 02:49:43,554] [INFO] Query marker FASTA was written to OceanDNA-b40594/markers.fasta
[2023-03-17 02:49:43,554] [INFO] Task started: Blastn
[2023-03-17 02:49:43,554] [INFO] Running command: blastn -query OceanDNA-b40594/markers.fasta -db /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/reference_markers.fasta -out OceanDNA-b40594/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:49:44,060] [INFO] Task succeeded: Blastn
[2023-03-17 02:49:44,060] [INFO] Selected 16 target genomes.
[2023-03-17 02:49:44,061] [INFO] Target genome list was writen to OceanDNA-b40594/target_genomes.txt
[2023-03-17 02:49:44,220] [INFO] Task started: fastANI
[2023-03-17 02:49:44,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg29e376c6-6ca5-44ea-8dea-4634e0223e45/OceanDNA-b40594.fa --refList OceanDNA-b40594/target_genomes.txt --output OceanDNA-b40594/fastani_result.tsv --threads 1
[2023-03-17 02:49:52,870] [INFO] Task succeeded: fastANI
[2023-03-17 02:49:52,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:49:52,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:49:52,871] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:49:52,871] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:49:52,871] [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
--------------------------------------------------------------------------------
[2023-03-17 02:49:52,871] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40594/tc_result.tsv
[2023-03-17 02:49:52,871] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:49:52,872] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:49:52,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/checkm_data
[2023-03-17 02:49:52,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:49:52,877] [INFO] Task started: CheckM
[2023-03-17 02:49:52,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40594/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40594/checkm_input OceanDNA-b40594/checkm_result
[2023-03-17 02:50:11,274] [INFO] Task succeeded: CheckM
[2023-03-17 02:50:11,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.02%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:50:11,277] [INFO] ===== Completeness check finished =====
[2023-03-17 02:50:11,278] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:50:11,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40594/markers.fasta)
[2023-03-17 02:50:11,279] [INFO] Task started: Blastn
[2023-03-17 02:50:11,279] [INFO] Running command: blastn -query OceanDNA-b40594/markers.fasta -db /var/lib/cwl/stge82bbb50-b7e0-46f0-baf5-47ad13d43dd8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40594/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:11,998] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:12,002] [INFO] Selected 24 target genomes.
[2023-03-17 02:50:12,002] [INFO] Target genome list was writen to OceanDNA-b40594/target_genomes_gtdb.txt
[2023-03-17 02:50:12,072] [INFO] Task started: fastANI
[2023-03-17 02:50:12,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg29e376c6-6ca5-44ea-8dea-4634e0223e45/OceanDNA-b40594.fa --refList OceanDNA-b40594/target_genomes_gtdb.txt --output OceanDNA-b40594/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:50:19,417] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:19,420] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:50:19,421] [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_902591495.1	s__UBA9145 sp902591495	84.2562	173	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727755.1	s__UBA9145 sp002727755	84.177	166	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	97.64	97.41	0.73	0.73	3	-
GCA_002714195.1	s__UBA9145 sp002714195	76.9724	62	245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:50:19,422] [INFO] GTDB search result was written to OceanDNA-b40594/result_gtdb.tsv
[2023-03-17 02:50:19,423] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:50:19,425] [INFO] DFAST_QC result json was written to OceanDNA-b40594/dqc_result.json
[2023-03-17 02:50:19,425] [INFO] DFAST_QC completed!
[2023-03-17 02:50:19,425] [INFO] Total running time: 0h0m42s