[2023-03-15 13:39:34,879] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:39:34,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:39:34,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference
[2023-03-15 13:39:37,060] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:39:37,060] [INFO] Task started: Prodigal
[2023-03-15 13:39:37,060] [INFO] Running command: cat /var/lib/cwl/stge82d5bce-b792-41e1-92b9-c8c002955664/OceanDNA-b33099.fa | prodigal -d OceanDNA-b33099/cds.fna -a OceanDNA-b33099/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:39:53,183] [INFO] Task succeeded: Prodigal
[2023-03-15 13:39:53,183] [INFO] Task started: HMMsearch
[2023-03-15 13:39:53,183] [INFO] Running command: hmmsearch --tblout OceanDNA-b33099/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/reference_markers.hmm OceanDNA-b33099/protein.faa > /dev/null
[2023-03-15 13:39:53,346] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:39:53,347] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge82d5bce-b792-41e1-92b9-c8c002955664/OceanDNA-b33099.fa]
[2023-03-15 13:39:53,376] [INFO] Query marker FASTA was written to OceanDNA-b33099/markers.fasta
[2023-03-15 13:39:53,378] [INFO] Task started: Blastn
[2023-03-15 13:39:53,378] [INFO] Running command: blastn -query OceanDNA-b33099/markers.fasta -db /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/reference_markers.fasta -out OceanDNA-b33099/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:39:53,906] [INFO] Task succeeded: Blastn
[2023-03-15 13:39:53,910] [INFO] Selected 21 target genomes.
[2023-03-15 13:39:53,910] [INFO] Target genome list was writen to OceanDNA-b33099/target_genomes.txt
[2023-03-15 13:39:53,924] [INFO] Task started: fastANI
[2023-03-15 13:39:53,924] [INFO] Running command: fastANI --query /var/lib/cwl/stge82d5bce-b792-41e1-92b9-c8c002955664/OceanDNA-b33099.fa --refList OceanDNA-b33099/target_genomes.txt --output OceanDNA-b33099/fastani_result.tsv --threads 1
[2023-03-15 13:40:09,151] [INFO] Task succeeded: fastANI
[2023-03-15 13:40:09,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:40:09,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:40:09,152] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:40:09,152] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:40:09,152] [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 13:40:09,155] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33099/tc_result.tsv
[2023-03-15 13:40:09,157] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:40:09,157] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:40:09,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/checkm_data
[2023-03-15 13:40:09,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:40:09,184] [INFO] Task started: CheckM
[2023-03-15 13:40:09,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33099/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33099/checkm_input OceanDNA-b33099/checkm_result
[2023-03-15 13:40:51,931] [INFO] Task succeeded: CheckM
[2023-03-15 13:40:51,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.43%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 13:40:51,995] [INFO] ===== Completeness check finished =====
[2023-03-15 13:40:51,995] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:40:51,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33099/markers.fasta)
[2023-03-15 13:40:51,996] [INFO] Task started: Blastn
[2023-03-15 13:40:51,996] [INFO] Running command: blastn -query OceanDNA-b33099/markers.fasta -db /var/lib/cwl/stg6b913740-1485-44ae-a6e2-403e82bdc769/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33099/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:40:52,706] [INFO] Task succeeded: Blastn
[2023-03-15 13:40:52,711] [INFO] Selected 22 target genomes.
[2023-03-15 13:40:52,711] [INFO] Target genome list was writen to OceanDNA-b33099/target_genomes_gtdb.txt
[2023-03-15 13:40:52,808] [INFO] Task started: fastANI
[2023-03-15 13:40:52,808] [INFO] Running command: fastANI --query /var/lib/cwl/stge82d5bce-b792-41e1-92b9-c8c002955664/OceanDNA-b33099.fa --refList OceanDNA-b33099/target_genomes_gtdb.txt --output OceanDNA-b33099/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:41:10,564] [INFO] Task succeeded: fastANI
[2023-03-15 13:41:10,566] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:41:10,567] [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_002434595.1	s__UBA6544 sp002434595	92.3342	497	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665505.1	s__UBA6544 sp018665505	76.1803	131	854	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__UBA6544	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:41:10,568] [INFO] GTDB search result was written to OceanDNA-b33099/result_gtdb.tsv
[2023-03-15 13:41:10,571] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:41:10,574] [INFO] DFAST_QC result json was written to OceanDNA-b33099/dqc_result.json
[2023-03-15 13:41:10,574] [INFO] DFAST_QC completed!
[2023-03-15 13:41:10,574] [INFO] Total running time: 0h1m36s