[2023-03-19 01:36:41,347] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:36:41,347] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:36:41,347] [INFO] DQC Reference Directory: /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference
[2023-03-19 01:36:42,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:36:42,457] [INFO] Task started: Prodigal
[2023-03-19 01:36:42,457] [INFO] Running command: cat /var/lib/cwl/stga11df554-bdf7-486f-b71a-8c2362253e7a/OceanDNA-b36186.fa | prodigal -d OceanDNA-b36186/cds.fna -a OceanDNA-b36186/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:36:49,306] [INFO] Task succeeded: Prodigal
[2023-03-19 01:36:49,307] [INFO] Task started: HMMsearch
[2023-03-19 01:36:49,307] [INFO] Running command: hmmsearch --tblout OceanDNA-b36186/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/reference_markers.hmm OceanDNA-b36186/protein.faa > /dev/null
[2023-03-19 01:36:49,472] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:36:49,472] [INFO] Found 6/6 markers.
[2023-03-19 01:36:49,482] [INFO] Query marker FASTA was written to OceanDNA-b36186/markers.fasta
[2023-03-19 01:36:49,483] [INFO] Task started: Blastn
[2023-03-19 01:36:49,484] [INFO] Running command: blastn -query OceanDNA-b36186/markers.fasta -db /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/reference_markers.fasta -out OceanDNA-b36186/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:36:50,054] [INFO] Task succeeded: Blastn
[2023-03-19 01:36:50,055] [INFO] Selected 29 target genomes.
[2023-03-19 01:36:50,055] [INFO] Target genome list was writen to OceanDNA-b36186/target_genomes.txt
[2023-03-19 01:36:50,075] [INFO] Task started: fastANI
[2023-03-19 01:36:50,075] [INFO] Running command: fastANI --query /var/lib/cwl/stga11df554-bdf7-486f-b71a-8c2362253e7a/OceanDNA-b36186.fa --refList OceanDNA-b36186/target_genomes.txt --output OceanDNA-b36186/fastani_result.tsv --threads 1
[2023-03-19 01:37:06,064] [INFO] Task succeeded: fastANI
[2023-03-19 01:37:06,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:37:06,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:37:06,064] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:37:06,064] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:37:06,065] [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
--------------------------------------------------------------------------------
[2023-03-19 01:37:06,065] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36186/tc_result.tsv
[2023-03-19 01:37:06,509] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:37:06,509] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:37:06,509] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/checkm_data
[2023-03-19 01:37:06,512] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:37:06,596] [INFO] Task started: CheckM
[2023-03-19 01:37:06,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36186/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36186/checkm_input OceanDNA-b36186/checkm_result
[2023-03-19 01:37:28,634] [INFO] Task succeeded: CheckM
[2023-03-19 01:37:28,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:37:28,636] [INFO] ===== Completeness check finished =====
[2023-03-19 01:37:28,636] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:37:28,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36186/markers.fasta)
[2023-03-19 01:37:28,638] [INFO] Task started: Blastn
[2023-03-19 01:37:28,638] [INFO] Running command: blastn -query OceanDNA-b36186/markers.fasta -db /var/lib/cwl/stgea7f8fb4-3c91-4cde-9ad7-38d00075a4a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36186/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:37:29,534] [INFO] Task succeeded: Blastn
[2023-03-19 01:37:29,535] [INFO] Selected 19 target genomes.
[2023-03-19 01:37:29,535] [INFO] Target genome list was writen to OceanDNA-b36186/target_genomes_gtdb.txt
[2023-03-19 01:37:29,550] [INFO] Task started: fastANI
[2023-03-19 01:37:29,550] [INFO] Running command: fastANI --query /var/lib/cwl/stga11df554-bdf7-486f-b71a-8c2362253e7a/OceanDNA-b36186.fa --refList OceanDNA-b36186/target_genomes_gtdb.txt --output OceanDNA-b36186/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:37:37,428] [INFO] Task succeeded: fastANI
[2023-03-19 01:37:37,434] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:37:37,434] [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_905181885.1	s__GCA-002733105 sp905181885	95.0526	409	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905479985.1	s__GCA-002733105 sp905479985	78.0634	113	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479075.1	s__GCA-002733105 sp905479075	77.7796	92	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018646825.1	s__GCA-002733105 sp018646825	77.4752	103	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859375.1	s__GCA-002733105 sp014859375	77.2987	66	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163085.1	s__41-12-T18 sp002163085	77.0607	58	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__41-12-T18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215825.1	s__GCA-002733105 sp013215825	76.9156	64	416	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__GCA-002733105	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:37:37,434] [INFO] GTDB search result was written to OceanDNA-b36186/result_gtdb.tsv
[2023-03-19 01:37:37,434] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:37:37,435] [INFO] DFAST_QC result json was written to OceanDNA-b36186/dqc_result.json
[2023-03-19 01:37:37,435] [INFO] DFAST_QC completed!
[2023-03-19 01:37:37,435] [INFO] Total running time: 0h0m56s