[2023-03-18 05:35:37,309] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference
[2023-03-18 05:35:38,961] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,962] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,963] [INFO] Running command: cat /var/lib/cwl/stgc78845ef-9ad7-4dc1-bb23-300777d96dc8/OceanDNA-b32844.fa | prodigal -d OceanDNA-b32844/cds.fna -a OceanDNA-b32844/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:35:48,576] [INFO] Task succeeded: Prodigal
[2023-03-18 05:35:48,576] [INFO] Task started: HMMsearch
[2023-03-18 05:35:48,576] [INFO] Running command: hmmsearch --tblout OceanDNA-b32844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/reference_markers.hmm OceanDNA-b32844/protein.faa > /dev/null
[2023-03-18 05:35:48,752] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:35:48,752] [INFO] Found 6/6 markers.
[2023-03-18 05:35:48,769] [INFO] Query marker FASTA was written to OceanDNA-b32844/markers.fasta
[2023-03-18 05:35:48,770] [INFO] Task started: Blastn
[2023-03-18 05:35:48,771] [INFO] Running command: blastn -query OceanDNA-b32844/markers.fasta -db /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/reference_markers.fasta -out OceanDNA-b32844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:35:49,341] [INFO] Task succeeded: Blastn
[2023-03-18 05:35:49,343] [INFO] Selected 19 target genomes.
[2023-03-18 05:35:49,343] [INFO] Target genome list was writen to OceanDNA-b32844/target_genomes.txt
[2023-03-18 05:35:49,356] [INFO] Task started: fastANI
[2023-03-18 05:35:49,356] [INFO] Running command: fastANI --query /var/lib/cwl/stgc78845ef-9ad7-4dc1-bb23-300777d96dc8/OceanDNA-b32844.fa --refList OceanDNA-b32844/target_genomes.txt --output OceanDNA-b32844/fastani_result.tsv --threads 1
[2023-03-18 05:36:01,227] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:01,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:01,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:01,228] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:01,228] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 05:36:01,228] [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
--------------------------------------------------------------------------------
[2023-03-18 05:36:01,228] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32844/tc_result.tsv
[2023-03-18 05:36:01,228] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:01,228] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:01,228] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/checkm_data
[2023-03-18 05:36:01,231] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:01,237] [INFO] Task started: CheckM
[2023-03-18 05:36:01,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32844/checkm_input OceanDNA-b32844/checkm_result
[2023-03-18 05:36:30,276] [INFO] Task succeeded: CheckM
[2023-03-18 05:36:30,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.29%
Contamintation: 5.15%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 05:36:30,327] [INFO] ===== Completeness check finished =====
[2023-03-18 05:36:30,327] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:36:30,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32844/markers.fasta)
[2023-03-18 05:36:30,329] [INFO] Task started: Blastn
[2023-03-18 05:36:30,329] [INFO] Running command: blastn -query OceanDNA-b32844/markers.fasta -db /var/lib/cwl/stgb59513a9-ff28-42aa-bc21-1d38c7b57b89/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:31,272] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:31,273] [INFO] Selected 24 target genomes.
[2023-03-18 05:36:31,274] [INFO] Target genome list was writen to OceanDNA-b32844/target_genomes_gtdb.txt
[2023-03-18 05:36:31,320] [INFO] Task started: fastANI
[2023-03-18 05:36:31,320] [INFO] Running command: fastANI --query /var/lib/cwl/stgc78845ef-9ad7-4dc1-bb23-300777d96dc8/OceanDNA-b32844.fa --refList OceanDNA-b32844/target_genomes_gtdb.txt --output OceanDNA-b32844/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:36:41,798] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:41,801] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:36:41,801] [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_002937585.1	s__MarineAlpha9-Bin7 sp002937585	90.418	445	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__MarineAlpha9-Bin7	95.0	99.30	99.21	0.83	0.71	7	-
GCA_002938115.1	s__MarineAlpha9-Bin7 sp002938115	77.4092	99	527	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA7887;f__UBA7887;g__MarineAlpha9-Bin7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:36:41,802] [INFO] GTDB search result was written to OceanDNA-b32844/result_gtdb.tsv
[2023-03-18 05:36:41,802] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:36:41,802] [INFO] DFAST_QC result json was written to OceanDNA-b32844/dqc_result.json
[2023-03-18 05:36:41,802] [INFO] DFAST_QC completed!
[2023-03-18 05:36:41,802] [INFO] Total running time: 0h1m4s