[2023-03-18 00:15:08,418] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:15:08,418] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:15:08,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference
[2023-03-18 00:15:09,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:15:09,528] [INFO] Task started: Prodigal
[2023-03-18 00:15:09,528] [INFO] Running command: cat /var/lib/cwl/stge45b6fc5-4fbe-45f3-8931-472a199ff03e/OceanDNA-b32482.fa | prodigal -d OceanDNA-b32482/cds.fna -a OceanDNA-b32482/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:15:12,757] [INFO] Task succeeded: Prodigal
[2023-03-18 00:15:12,757] [INFO] Task started: HMMsearch
[2023-03-18 00:15:12,757] [INFO] Running command: hmmsearch --tblout OceanDNA-b32482/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/reference_markers.hmm OceanDNA-b32482/protein.faa > /dev/null
[2023-03-18 00:15:12,905] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:15:12,905] [INFO] Found 6/6 markers.
[2023-03-18 00:15:12,915] [INFO] Query marker FASTA was written to OceanDNA-b32482/markers.fasta
[2023-03-18 00:15:12,915] [INFO] Task started: Blastn
[2023-03-18 00:15:12,915] [INFO] Running command: blastn -query OceanDNA-b32482/markers.fasta -db /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/reference_markers.fasta -out OceanDNA-b32482/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:13,419] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:13,420] [INFO] Selected 17 target genomes.
[2023-03-18 00:15:13,420] [INFO] Target genome list was writen to OceanDNA-b32482/target_genomes.txt
[2023-03-18 00:15:13,427] [INFO] Task started: fastANI
[2023-03-18 00:15:13,427] [INFO] Running command: fastANI --query /var/lib/cwl/stge45b6fc5-4fbe-45f3-8931-472a199ff03e/OceanDNA-b32482.fa --refList OceanDNA-b32482/target_genomes.txt --output OceanDNA-b32482/fastani_result.tsv --threads 1
[2023-03-18 00:15:23,624] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:23,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:15:23,624] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:15:23,625] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:15:23,625] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:15:23,625] [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 00:15:23,625] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32482/tc_result.tsv
[2023-03-18 00:15:23,625] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:15:23,625] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:15:23,625] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/checkm_data
[2023-03-18 00:15:23,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:15:23,635] [INFO] Task started: CheckM
[2023-03-18 00:15:23,636] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32482/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32482/checkm_input OceanDNA-b32482/checkm_result
[2023-03-18 00:15:38,469] [INFO] Task succeeded: CheckM
[2023-03-18 00:15:38,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.09%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:15:38,512] [INFO] ===== Completeness check finished =====
[2023-03-18 00:15:38,512] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:15:38,512] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32482/markers.fasta)
[2023-03-18 00:15:38,513] [INFO] Task started: Blastn
[2023-03-18 00:15:38,513] [INFO] Running command: blastn -query OceanDNA-b32482/markers.fasta -db /var/lib/cwl/stg1f277e46-cf21-4432-94f8-909a25e0fde7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32482/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:15:39,208] [INFO] Task succeeded: Blastn
[2023-03-18 00:15:39,209] [INFO] Selected 14 target genomes.
[2023-03-18 00:15:39,209] [INFO] Target genome list was writen to OceanDNA-b32482/target_genomes_gtdb.txt
[2023-03-18 00:15:39,227] [INFO] Task started: fastANI
[2023-03-18 00:15:39,227] [INFO] Running command: fastANI --query /var/lib/cwl/stge45b6fc5-4fbe-45f3-8931-472a199ff03e/OceanDNA-b32482.fa --refList OceanDNA-b32482/target_genomes_gtdb.txt --output OceanDNA-b32482/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:15:41,960] [INFO] Task succeeded: fastANI
[2023-03-18 00:15:41,964] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:15:41,964] [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_002690625.1	s__MED722 sp002690625	99.9677	99	168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__MED722	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902579545.1	s__CACHHO01 sp902579545	77.3012	56	168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__CACHHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902615805.1	s__TMED62 sp902615805	77.0382	56	168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002170595.1	s__TMED62 sp002170595	77.0044	60	168	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__TMED109;f__TMED131;g__TMED62	95.0	99.91	99.91	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:15:41,971] [INFO] GTDB search result was written to OceanDNA-b32482/result_gtdb.tsv
[2023-03-18 00:15:41,975] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:15:41,976] [INFO] DFAST_QC result json was written to OceanDNA-b32482/dqc_result.json
[2023-03-18 00:15:41,976] [INFO] DFAST_QC completed!
[2023-03-18 00:15:41,976] [INFO] Total running time: 0h0m34s