[2023-03-16 10:07:19,368] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:07:19,368] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:07:19,369] [INFO] DQC Reference Directory: /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference
[2023-03-16 10:07:20,495] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:07:20,495] [INFO] Task started: Prodigal
[2023-03-16 10:07:20,495] [INFO] Running command: cat /var/lib/cwl/stgd0f86a79-c383-4046-8dc2-b5e80ae49fba/OceanDNA-b33055.fa | prodigal -d OceanDNA-b33055/cds.fna -a OceanDNA-b33055/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:07:40,537] [INFO] Task succeeded: Prodigal
[2023-03-16 10:07:40,537] [INFO] Task started: HMMsearch
[2023-03-16 10:07:40,537] [INFO] Running command: hmmsearch --tblout OceanDNA-b33055/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/reference_markers.hmm OceanDNA-b33055/protein.faa > /dev/null
[2023-03-16 10:07:40,737] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:07:40,737] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd0f86a79-c383-4046-8dc2-b5e80ae49fba/OceanDNA-b33055.fa]
[2023-03-16 10:07:40,763] [INFO] Query marker FASTA was written to OceanDNA-b33055/markers.fasta
[2023-03-16 10:07:40,763] [INFO] Task started: Blastn
[2023-03-16 10:07:40,763] [INFO] Running command: blastn -query OceanDNA-b33055/markers.fasta -db /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/reference_markers.fasta -out OceanDNA-b33055/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:07:41,367] [INFO] Task succeeded: Blastn
[2023-03-16 10:07:41,368] [INFO] Selected 25 target genomes.
[2023-03-16 10:07:41,369] [INFO] Target genome list was writen to OceanDNA-b33055/target_genomes.txt
[2023-03-16 10:07:41,382] [INFO] Task started: fastANI
[2023-03-16 10:07:41,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f86a79-c383-4046-8dc2-b5e80ae49fba/OceanDNA-b33055.fa --refList OceanDNA-b33055/target_genomes.txt --output OceanDNA-b33055/fastani_result.tsv --threads 1
[2023-03-16 10:07:56,314] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:56,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:07:56,315] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:07:56,315] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:07:56,315] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:07:56,315] [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 10:07:56,315] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33055/tc_result.tsv
[2023-03-16 10:07:56,316] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:07:56,316] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:07:56,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/checkm_data
[2023-03-16 10:07:56,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:07:56,324] [INFO] Task started: CheckM
[2023-03-16 10:07:56,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33055/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33055/checkm_input OceanDNA-b33055/checkm_result
[2023-03-16 10:08:47,376] [INFO] Task succeeded: CheckM
[2023-03-16 10:08:47,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:08:47,380] [INFO] ===== Completeness check finished =====
[2023-03-16 10:08:47,380] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:08:47,380] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33055/markers.fasta)
[2023-03-16 10:08:47,381] [INFO] Task started: Blastn
[2023-03-16 10:08:47,381] [INFO] Running command: blastn -query OceanDNA-b33055/markers.fasta -db /var/lib/cwl/stgec6c124b-6053-4f35-b707-7ad9b07abf37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33055/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:48,403] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:48,404] [INFO] Selected 26 target genomes.
[2023-03-16 10:08:48,404] [INFO] Target genome list was writen to OceanDNA-b33055/target_genomes_gtdb.txt
[2023-03-16 10:08:48,502] [INFO] Task started: fastANI
[2023-03-16 10:08:48,502] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0f86a79-c383-4046-8dc2-b5e80ae49fba/OceanDNA-b33055.fa --refList OceanDNA-b33055/target_genomes_gtdb.txt --output OceanDNA-b33055/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:05,617] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:05,620] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:09:05,620] [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_002717185.1	s__GCA-2717185 sp002717185	77.851	297	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103325.1	s__GCA-2717185 sp012103325	76.3874	194	1108	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:09:05,620] [INFO] GTDB search result was written to OceanDNA-b33055/result_gtdb.tsv
[2023-03-16 10:09:05,620] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:05,621] [INFO] DFAST_QC result json was written to OceanDNA-b33055/dqc_result.json
[2023-03-16 10:09:05,621] [INFO] DFAST_QC completed!
[2023-03-16 10:09:05,621] [INFO] Total running time: 0h1m46s