[2023-03-14 13:27:20,527] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:27:20,527] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:27:20,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference
[2023-03-14 13:27:21,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:27:21,862] [INFO] Task started: Prodigal
[2023-03-14 13:27:21,863] [INFO] Running command: cat /var/lib/cwl/stgdb99023b-aa3e-41ed-a443-21f45f7a70c0/OceanDNA-b40222.fa | prodigal -d OceanDNA-b40222/cds.fna -a OceanDNA-b40222/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:27:33,201] [INFO] Task succeeded: Prodigal
[2023-03-14 13:27:33,202] [INFO] Task started: HMMsearch
[2023-03-14 13:27:33,202] [INFO] Running command: hmmsearch --tblout OceanDNA-b40222/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/reference_markers.hmm OceanDNA-b40222/protein.faa > /dev/null
[2023-03-14 13:27:33,396] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:27:33,397] [INFO] Found 6/6 markers.
[2023-03-14 13:27:33,413] [INFO] Query marker FASTA was written to OceanDNA-b40222/markers.fasta
[2023-03-14 13:27:33,413] [INFO] Task started: Blastn
[2023-03-14 13:27:33,414] [INFO] Running command: blastn -query OceanDNA-b40222/markers.fasta -db /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/reference_markers.fasta -out OceanDNA-b40222/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:27:34,015] [INFO] Task succeeded: Blastn
[2023-03-14 13:27:34,016] [INFO] Selected 23 target genomes.
[2023-03-14 13:27:34,016] [INFO] Target genome list was writen to OceanDNA-b40222/target_genomes.txt
[2023-03-14 13:27:34,032] [INFO] Task started: fastANI
[2023-03-14 13:27:34,032] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb99023b-aa3e-41ed-a443-21f45f7a70c0/OceanDNA-b40222.fa --refList OceanDNA-b40222/target_genomes.txt --output OceanDNA-b40222/fastani_result.tsv --threads 1
[2023-03-14 13:27:48,705] [INFO] Task succeeded: fastANI
[2023-03-14 13:27:48,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:27:48,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:27:48,706] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:27:48,706] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:27:48,706] [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
--------------------------------------------------------------------------------
[2023-03-14 13:27:48,706] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40222/tc_result.tsv
[2023-03-14 13:27:48,706] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:27:48,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:27:48,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/checkm_data
[2023-03-14 13:27:48,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:27:48,986] [INFO] Task started: CheckM
[2023-03-14 13:27:48,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40222/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40222/checkm_input OceanDNA-b40222/checkm_result
[2023-03-14 13:28:32,801] [INFO] Task succeeded: CheckM
[2023-03-14 13:28:32,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:28:32,804] [INFO] ===== Completeness check finished =====
[2023-03-14 13:28:32,805] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:28:32,805] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40222/markers.fasta)
[2023-03-14 13:28:32,806] [INFO] Task started: Blastn
[2023-03-14 13:28:32,806] [INFO] Running command: blastn -query OceanDNA-b40222/markers.fasta -db /var/lib/cwl/stgb5ba3d56-d7e7-45dd-89c8-6b9c6aea641d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40222/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:28:33,942] [INFO] Task succeeded: Blastn
[2023-03-14 13:28:33,944] [INFO] Selected 13 target genomes.
[2023-03-14 13:28:33,944] [INFO] Target genome list was writen to OceanDNA-b40222/target_genomes_gtdb.txt
[2023-03-14 13:28:33,961] [INFO] Task started: fastANI
[2023-03-14 13:28:33,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb99023b-aa3e-41ed-a443-21f45f7a70c0/OceanDNA-b40222.fa --refList OceanDNA-b40222/target_genomes_gtdb.txt --output OceanDNA-b40222/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:28:41,534] [INFO] Task succeeded: fastANI
[2023-03-14 13:28:41,537] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:28:41,538] [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_002701765.1	s__TMED48 sp002701765	98.0987	475	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	97.58	97.58	0.65	0.65	2	conclusive
GCA_002591625.1	s__TMED48 sp002591625	93.3775	513	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557735.1	s__TMED48 sp902557735	80.802	294	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692165.1	s__TMED48 sp002692165	80.4909	247	655	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__TMED48	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:28:41,538] [INFO] GTDB search result was written to OceanDNA-b40222/result_gtdb.tsv
[2023-03-14 13:28:41,538] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:28:41,539] [INFO] DFAST_QC result json was written to OceanDNA-b40222/dqc_result.json
[2023-03-14 13:28:41,539] [INFO] DFAST_QC completed!
[2023-03-14 13:28:41,539] [INFO] Total running time: 0h1m21s