[2023-03-16 07:49:29,132] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:29,132] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:29,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference
[2023-03-16 07:49:30,899] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:30,900] [INFO] Task started: Prodigal
[2023-03-16 07:49:30,900] [INFO] Running command: cat /var/lib/cwl/stg3870ddd0-a901-4ec5-a226-43c2e707cd41/OceanDNA-b35448.fa | prodigal -d OceanDNA-b35448/cds.fna -a OceanDNA-b35448/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:34,795] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:34,795] [INFO] Task started: HMMsearch
[2023-03-16 07:49:34,795] [INFO] Running command: hmmsearch --tblout OceanDNA-b35448/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/reference_markers.hmm OceanDNA-b35448/protein.faa > /dev/null
[2023-03-16 07:49:35,006] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:35,007] [INFO] Found 6/6 markers.
[2023-03-16 07:49:35,014] [INFO] Query marker FASTA was written to OceanDNA-b35448/markers.fasta
[2023-03-16 07:49:35,014] [INFO] Task started: Blastn
[2023-03-16 07:49:35,015] [INFO] Running command: blastn -query OceanDNA-b35448/markers.fasta -db /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/reference_markers.fasta -out OceanDNA-b35448/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:37,635] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:37,636] [INFO] Selected 25 target genomes.
[2023-03-16 07:49:37,636] [INFO] Target genome list was writen to OceanDNA-b35448/target_genomes.txt
[2023-03-16 07:49:37,654] [INFO] Task started: fastANI
[2023-03-16 07:49:37,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg3870ddd0-a901-4ec5-a226-43c2e707cd41/OceanDNA-b35448.fa --refList OceanDNA-b35448/target_genomes.txt --output OceanDNA-b35448/fastani_result.tsv --threads 1
[2023-03-16 07:49:47,244] [INFO] Task succeeded: fastANI
[2023-03-16 07:49:47,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:49:47,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:49:47,245] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:49:47,245] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:49:47,245] [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 07:49:47,245] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35448/tc_result.tsv
[2023-03-16 07:49:47,245] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:49:47,245] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:49:47,245] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/checkm_data
[2023-03-16 07:49:47,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:49:47,258] [INFO] Task started: CheckM
[2023-03-16 07:49:47,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35448/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35448/checkm_input OceanDNA-b35448/checkm_result
[2023-03-16 07:50:09,014] [INFO] Task succeeded: CheckM
[2023-03-16 07:50:09,015] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:50:09,016] [INFO] ===== Completeness check finished =====
[2023-03-16 07:50:09,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:50:09,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35448/markers.fasta)
[2023-03-16 07:50:09,018] [INFO] Task started: Blastn
[2023-03-16 07:50:09,018] [INFO] Running command: blastn -query OceanDNA-b35448/markers.fasta -db /var/lib/cwl/stg47030f7c-708c-490a-ab99-475d9225c18f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35448/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:50:10,792] [INFO] Task succeeded: Blastn
[2023-03-16 07:50:10,793] [INFO] Selected 18 target genomes.
[2023-03-16 07:50:10,793] [INFO] Target genome list was writen to OceanDNA-b35448/target_genomes_gtdb.txt
[2023-03-16 07:50:10,950] [INFO] Task started: fastANI
[2023-03-16 07:50:10,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg3870ddd0-a901-4ec5-a226-43c2e707cd41/OceanDNA-b35448.fa --refList OceanDNA-b35448/target_genomes_gtdb.txt --output OceanDNA-b35448/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:50:14,280] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:14,284] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:50:14,284] [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_902559815.1	s__GCA-2705445 sp902559815	99.5907	201	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018674175.1	s__GCA-2705445 sp018674175	77.423	132	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	99.85	99.83	0.95	0.93	3	-
GCA_002705445.1	s__GCA-2705445 sp002705445	77.2638	105	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	97.03	97.03	0.89	0.89	2	-
GCA_902624655.1	s__GCA-2705445 sp902624655	76.8911	91	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-002705445;f__GCA-002705445;g__GCA-2705445	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:50:14,284] [INFO] GTDB search result was written to OceanDNA-b35448/result_gtdb.tsv
[2023-03-16 07:50:14,284] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:50:14,285] [INFO] DFAST_QC result json was written to OceanDNA-b35448/dqc_result.json
[2023-03-16 07:50:14,285] [INFO] DFAST_QC completed!
[2023-03-16 07:50:14,285] [INFO] Total running time: 0h0m45s