[2023-03-18 09:26:42,703] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,703] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,703] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference
[2023-03-18 09:26:43,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,799] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,799] [INFO] Running command: cat /var/lib/cwl/stg69dbf8e1-ba03-481e-b966-d82104a3eb3b/OceanDNA-b28629.fa | prodigal -d OceanDNA-b28629/cds.fna -a OceanDNA-b28629/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:26:53,378] [INFO] Task succeeded: Prodigal
[2023-03-18 09:26:53,378] [INFO] Task started: HMMsearch
[2023-03-18 09:26:53,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b28629/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/reference_markers.hmm OceanDNA-b28629/protein.faa > /dev/null
[2023-03-18 09:26:53,556] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:26:53,557] [INFO] Found 6/6 markers.
[2023-03-18 09:26:53,573] [INFO] Query marker FASTA was written to OceanDNA-b28629/markers.fasta
[2023-03-18 09:26:53,573] [INFO] Task started: Blastn
[2023-03-18 09:26:53,574] [INFO] Running command: blastn -query OceanDNA-b28629/markers.fasta -db /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/reference_markers.fasta -out OceanDNA-b28629/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:26:54,175] [INFO] Task succeeded: Blastn
[2023-03-18 09:26:54,176] [INFO] Selected 36 target genomes.
[2023-03-18 09:26:54,176] [INFO] Target genome list was writen to OceanDNA-b28629/target_genomes.txt
[2023-03-18 09:26:54,214] [INFO] Task started: fastANI
[2023-03-18 09:26:54,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg69dbf8e1-ba03-481e-b966-d82104a3eb3b/OceanDNA-b28629.fa --refList OceanDNA-b28629/target_genomes.txt --output OceanDNA-b28629/fastani_result.tsv --threads 1
[2023-03-18 09:27:14,676] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:14,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:14,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:14,677] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:27:14,677] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:27:14,677] [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
--------------------------------------------------------------------------------
[2023-03-18 09:27:14,678] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28629/tc_result.tsv
[2023-03-18 09:27:14,678] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:14,678] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:14,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/checkm_data
[2023-03-18 09:27:14,680] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:14,684] [INFO] Task started: CheckM
[2023-03-18 09:27:14,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28629/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28629/checkm_input OceanDNA-b28629/checkm_result
[2023-03-18 09:27:43,598] [INFO] Task succeeded: CheckM
[2023-03-18 09:27:43,598] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 1.50%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 09:27:43,600] [INFO] ===== Completeness check finished =====
[2023-03-18 09:27:43,600] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:27:43,601] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28629/markers.fasta)
[2023-03-18 09:27:43,601] [INFO] Task started: Blastn
[2023-03-18 09:27:43,601] [INFO] Running command: blastn -query OceanDNA-b28629/markers.fasta -db /var/lib/cwl/stg6f3c5966-d321-4228-bfe2-169e1924317f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28629/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:44,593] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:44,594] [INFO] Selected 24 target genomes.
[2023-03-18 09:27:44,594] [INFO] Target genome list was writen to OceanDNA-b28629/target_genomes_gtdb.txt
[2023-03-18 09:27:44,621] [INFO] Task started: fastANI
[2023-03-18 09:27:44,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg69dbf8e1-ba03-481e-b966-d82104a3eb3b/OceanDNA-b28629.fa --refList OceanDNA-b28629/target_genomes_gtdb.txt --output OceanDNA-b28629/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:27:57,551] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:57,553] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:27:57,553] [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_016778765.1	s__LGRT01 sp016778765	96.7865	412	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	98.26	96.00	0.81	0.61	8	conclusive
GCA_001642945.1	s__LGRT01 sp001642945	93.719	440	459	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	99.21	98.81	0.97	0.88	20	-
--------------------------------------------------------------------------------
[2023-03-18 09:27:57,554] [INFO] GTDB search result was written to OceanDNA-b28629/result_gtdb.tsv
[2023-03-18 09:27:57,554] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:27:57,554] [INFO] DFAST_QC result json was written to OceanDNA-b28629/dqc_result.json
[2023-03-18 09:27:57,554] [INFO] DFAST_QC completed!
[2023-03-18 09:27:57,554] [INFO] Total running time: 0h1m15s