[2023-03-15 06:35:36,163] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,165] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference
[2023-03-15 06:35:37,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,299] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,299] [INFO] Running command: cat /var/lib/cwl/stgaf5528dd-6b87-46db-8c7a-d85e880c9f42/OceanDNA-b34175.fa | prodigal -d OceanDNA-b34175/cds.fna -a OceanDNA-b34175/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:35:44,244] [INFO] Task succeeded: Prodigal
[2023-03-15 06:35:44,244] [INFO] Task started: HMMsearch
[2023-03-15 06:35:44,244] [INFO] Running command: hmmsearch --tblout OceanDNA-b34175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/reference_markers.hmm OceanDNA-b34175/protein.faa > /dev/null
[2023-03-15 06:35:44,412] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:35:44,413] [INFO] Found 6/6 markers.
[2023-03-15 06:35:44,436] [INFO] Query marker FASTA was written to OceanDNA-b34175/markers.fasta
[2023-03-15 06:35:44,436] [INFO] Task started: Blastn
[2023-03-15 06:35:44,436] [INFO] Running command: blastn -query OceanDNA-b34175/markers.fasta -db /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/reference_markers.fasta -out OceanDNA-b34175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:35:44,977] [INFO] Task succeeded: Blastn
[2023-03-15 06:35:44,981] [INFO] Selected 21 target genomes.
[2023-03-15 06:35:44,982] [INFO] Target genome list was writen to OceanDNA-b34175/target_genomes.txt
[2023-03-15 06:35:44,991] [INFO] Task started: fastANI
[2023-03-15 06:35:44,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5528dd-6b87-46db-8c7a-d85e880c9f42/OceanDNA-b34175.fa --refList OceanDNA-b34175/target_genomes.txt --output OceanDNA-b34175/fastani_result.tsv --threads 1
[2023-03-15 06:35:53,476] [INFO] Task succeeded: fastANI
[2023-03-15 06:35:53,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:35:53,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:35:53,477] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:35:53,477] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 06:35:53,477] [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
--------------------------------------------------------------------------------
[2023-03-15 06:35:53,478] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34175/tc_result.tsv
[2023-03-15 06:35:53,482] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:35:53,482] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:35:53,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/checkm_data
[2023-03-15 06:35:53,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:35:53,540] [INFO] Task started: CheckM
[2023-03-15 06:35:53,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34175/checkm_input OceanDNA-b34175/checkm_result
[2023-03-15 06:36:18,755] [INFO] Task succeeded: CheckM
[2023-03-15 06:36:18,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:36:18,759] [INFO] ===== Completeness check finished =====
[2023-03-15 06:36:18,760] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:36:18,760] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34175/markers.fasta)
[2023-03-15 06:36:18,761] [INFO] Task started: Blastn
[2023-03-15 06:36:18,762] [INFO] Running command: blastn -query OceanDNA-b34175/markers.fasta -db /var/lib/cwl/stg90dbf1d8-348b-40df-abb6-93d0196110f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:36:19,828] [INFO] Task succeeded: Blastn
[2023-03-15 06:36:19,835] [INFO] Selected 18 target genomes.
[2023-03-15 06:36:19,835] [INFO] Target genome list was writen to OceanDNA-b34175/target_genomes_gtdb.txt
[2023-03-15 06:36:19,882] [INFO] Task started: fastANI
[2023-03-15 06:36:19,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf5528dd-6b87-46db-8c7a-d85e880c9f42/OceanDNA-b34175.fa --refList OceanDNA-b34175/target_genomes_gtdb.txt --output OceanDNA-b34175/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:36:26,306] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:26,310] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 06:36:26,310] [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_002167745.1	s__UBA3031 sp002167745	99.6481	371	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	99.76	99.76	0.94	0.94	2	conclusive
GCA_009886305.1	s__UBA3031 sp009886305	82.1977	244	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478365.1	s__UBA3031 sp905478365	81.1372	249	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	98.56	98.18	0.78	0.69	7	-
GCA_002367635.1	s__UBA3031 sp002367635	77.393	70	393	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__UBA3031	95.0	99.64	99.62	0.86	0.85	3	-
--------------------------------------------------------------------------------
[2023-03-15 06:36:26,313] [INFO] GTDB search result was written to OceanDNA-b34175/result_gtdb.tsv
[2023-03-15 06:36:26,317] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:36:26,320] [INFO] DFAST_QC result json was written to OceanDNA-b34175/dqc_result.json
[2023-03-15 06:36:26,321] [INFO] DFAST_QC completed!
[2023-03-15 06:36:26,321] [INFO] Total running time: 0h0m50s