[2023-03-16 13:57:23,575] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:57:23,575] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:57:23,575] [INFO] DQC Reference Directory: /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference
[2023-03-16 13:57:26,812] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:57:26,812] [INFO] Task started: Prodigal
[2023-03-16 13:57:26,816] [INFO] Running command: cat /var/lib/cwl/stg5b0f8423-e681-4e1f-9b67-db5964f4baee/OceanDNA-b39352.fa | prodigal -d OceanDNA-b39352/cds.fna -a OceanDNA-b39352/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:57:36,024] [INFO] Task succeeded: Prodigal
[2023-03-16 13:57:36,024] [INFO] Task started: HMMsearch
[2023-03-16 13:57:36,024] [INFO] Running command: hmmsearch --tblout OceanDNA-b39352/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/reference_markers.hmm OceanDNA-b39352/protein.faa > /dev/null
[2023-03-16 13:57:36,278] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:57:36,279] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5b0f8423-e681-4e1f-9b67-db5964f4baee/OceanDNA-b39352.fa]
[2023-03-16 13:57:36,289] [INFO] Query marker FASTA was written to OceanDNA-b39352/markers.fasta
[2023-03-16 13:57:36,289] [INFO] Task started: Blastn
[2023-03-16 13:57:36,289] [INFO] Running command: blastn -query OceanDNA-b39352/markers.fasta -db /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/reference_markers.fasta -out OceanDNA-b39352/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:57:37,366] [INFO] Task succeeded: Blastn
[2023-03-16 13:57:37,367] [INFO] Selected 20 target genomes.
[2023-03-16 13:57:37,367] [INFO] Target genome list was writen to OceanDNA-b39352/target_genomes.txt
[2023-03-16 13:57:37,383] [INFO] Task started: fastANI
[2023-03-16 13:57:37,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0f8423-e681-4e1f-9b67-db5964f4baee/OceanDNA-b39352.fa --refList OceanDNA-b39352/target_genomes.txt --output OceanDNA-b39352/fastani_result.tsv --threads 1
[2023-03-16 13:57:55,872] [INFO] Task succeeded: fastANI
[2023-03-16 13:57:55,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:57:55,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:57:55,873] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:57:55,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 13:57:55,873] [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
--------------------------------------------------------------------------------
[2023-03-16 13:57:55,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39352/tc_result.tsv
[2023-03-16 13:57:55,873] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:57:55,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:57:55,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/checkm_data
[2023-03-16 13:57:55,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:57:55,880] [INFO] Task started: CheckM
[2023-03-16 13:57:55,880] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39352/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39352/checkm_input OceanDNA-b39352/checkm_result
[2023-03-16 13:58:29,492] [INFO] Task succeeded: CheckM
[2023-03-16 13:58:29,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.81%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 13:58:29,494] [INFO] ===== Completeness check finished =====
[2023-03-16 13:58:29,494] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:58:29,494] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39352/markers.fasta)
[2023-03-16 13:58:29,494] [INFO] Task started: Blastn
[2023-03-16 13:58:29,494] [INFO] Running command: blastn -query OceanDNA-b39352/markers.fasta -db /var/lib/cwl/stga289e904-a6c6-4d88-bb16-eda928bc9377/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39352/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:58:30,197] [INFO] Task succeeded: Blastn
[2023-03-16 13:58:30,198] [INFO] Selected 14 target genomes.
[2023-03-16 13:58:30,198] [INFO] Target genome list was writen to OceanDNA-b39352/target_genomes_gtdb.txt
[2023-03-16 13:58:30,805] [INFO] Task started: fastANI
[2023-03-16 13:58:30,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0f8423-e681-4e1f-9b67-db5964f4baee/OceanDNA-b39352.fa --refList OceanDNA-b39352/target_genomes_gtdb.txt --output OceanDNA-b39352/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:58:36,629] [INFO] Task succeeded: fastANI
[2023-03-16 13:58:36,636] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:58:36,636] [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_018607545.1	s__HTCC2207 sp018607545	87.2606	189	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000511875.1	s__HTCC2207 sp000511875	77.9401	164	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.9376	109	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_017858135.1	s__HTCC2207 sp017858135	77.8661	165	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_905478975.1	s__HTCC2207 sp905478975	77.7473	166	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.7145	153	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
GCA_002334915.1	s__HTCC2207 sp002334915	77.2557	97	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	76.9643	71	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664075.1	s__HTCC2207 sp018664075	76.9438	108	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	76.8254	98	404	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
--------------------------------------------------------------------------------
[2023-03-16 13:58:36,636] [INFO] GTDB search result was written to OceanDNA-b39352/result_gtdb.tsv
[2023-03-16 13:58:36,636] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:58:36,637] [INFO] DFAST_QC result json was written to OceanDNA-b39352/dqc_result.json
[2023-03-16 13:58:36,637] [INFO] DFAST_QC completed!
[2023-03-16 13:58:36,637] [INFO] Total running time: 0h1m13s