[2023-03-16 03:47:32,867] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,867] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,534] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,534] [INFO] Running command: cat /var/lib/cwl/stga8587e87-51ec-41f4-97b6-e2429c211085/OceanDNA-b29209.fa | prodigal -d OceanDNA-b29209/cds.fna -a OceanDNA-b29209/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:46,431] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:46,431] [INFO] Task started: HMMsearch
[2023-03-16 03:47:46,431] [INFO] Running command: hmmsearch --tblout OceanDNA-b29209/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/reference_markers.hmm OceanDNA-b29209/protein.faa > /dev/null
[2023-03-16 03:47:46,687] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:46,688] [INFO] Found 6/6 markers.
[2023-03-16 03:47:46,705] [INFO] Query marker FASTA was written to OceanDNA-b29209/markers.fasta
[2023-03-16 03:47:46,705] [INFO] Task started: Blastn
[2023-03-16 03:47:46,706] [INFO] Running command: blastn -query OceanDNA-b29209/markers.fasta -db /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/reference_markers.fasta -out OceanDNA-b29209/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:47,310] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:47,311] [INFO] Selected 29 target genomes.
[2023-03-16 03:47:47,311] [INFO] Target genome list was writen to OceanDNA-b29209/target_genomes.txt
[2023-03-16 03:47:47,327] [INFO] Task started: fastANI
[2023-03-16 03:47:47,327] [INFO] Running command: fastANI --query /var/lib/cwl/stga8587e87-51ec-41f4-97b6-e2429c211085/OceanDNA-b29209.fa --refList OceanDNA-b29209/target_genomes.txt --output OceanDNA-b29209/fastani_result.tsv --threads 1
[2023-03-16 03:48:03,914] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:03,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:03,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:03,915] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:03,915] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:48:03,915] [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 03:48:03,915] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29209/tc_result.tsv
[2023-03-16 03:48:03,915] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:03,915] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:03,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/checkm_data
[2023-03-16 03:48:03,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:03,922] [INFO] Task started: CheckM
[2023-03-16 03:48:03,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29209/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29209/checkm_input OceanDNA-b29209/checkm_result
[2023-03-16 03:48:37,574] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:37,575] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:37,577] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:37,577] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:37,577] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29209/markers.fasta)
[2023-03-16 03:48:37,577] [INFO] Task started: Blastn
[2023-03-16 03:48:37,577] [INFO] Running command: blastn -query OceanDNA-b29209/markers.fasta -db /var/lib/cwl/stg036588ee-84f4-4427-b45f-7206d44e9a66/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29209/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:38,477] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:38,478] [INFO] Selected 15 target genomes.
[2023-03-16 03:48:38,478] [INFO] Target genome list was writen to OceanDNA-b29209/target_genomes_gtdb.txt
[2023-03-16 03:48:38,554] [INFO] Task started: fastANI
[2023-03-16 03:48:38,554] [INFO] Running command: fastANI --query /var/lib/cwl/stga8587e87-51ec-41f4-97b6-e2429c211085/OceanDNA-b29209.fa --refList OceanDNA-b29209/target_genomes_gtdb.txt --output OceanDNA-b29209/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:43,384] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:43,389] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:48:43,389] [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_002711145.1	s__MED-G52 sp002711145	98.3177	391	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.17	95.57	0.64	0.63	3	conclusive
GCA_002682975.1	s__MED-G52 sp002682975	94.2612	270	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554885.1	s__MED-G52 sp902554885	81.8402	265	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.17	97.17	0.65	0.65	2	-
GCA_902635985.1	s__MED-G52 sp902635985	81.3078	295	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602765.1	s__MED-G52 sp902602765	81.2215	354	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	95.98	95.60	0.63	0.61	4	-
GCA_902631295.1	s__MED-G52 sp902631295	80.6879	368	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457055.1	s__MED-G52 sp002457055	79.553	415	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	96.90	95.38	0.85	0.77	11	-
GCA_001627925.1	s__MED-G52 sp001627925	79.4935	389	715	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.54	95.86	0.83	0.80	8	-
--------------------------------------------------------------------------------
[2023-03-16 03:48:43,390] [INFO] GTDB search result was written to OceanDNA-b29209/result_gtdb.tsv
[2023-03-16 03:48:43,390] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:43,390] [INFO] DFAST_QC result json was written to OceanDNA-b29209/dqc_result.json
[2023-03-16 03:48:43,391] [INFO] DFAST_QC completed!
[2023-03-16 03:48:43,391] [INFO] Total running time: 0h1m11s