[2023-03-15 07:08:26,145] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:08:26,145] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:08:26,145] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference
[2023-03-15 07:08:27,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:08:27,306] [INFO] Task started: Prodigal
[2023-03-15 07:08:27,306] [INFO] Running command: cat /var/lib/cwl/stg0660236b-89f8-43b4-8bc4-defad5e75e21/OceanDNA-b31321.fa | prodigal -d OceanDNA-b31321/cds.fna -a OceanDNA-b31321/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:08:29,894] [INFO] Task succeeded: Prodigal
[2023-03-15 07:08:29,894] [INFO] Task started: HMMsearch
[2023-03-15 07:08:29,894] [INFO] Running command: hmmsearch --tblout OceanDNA-b31321/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/reference_markers.hmm OceanDNA-b31321/protein.faa > /dev/null
[2023-03-15 07:08:30,029] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:08:30,029] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0660236b-89f8-43b4-8bc4-defad5e75e21/OceanDNA-b31321.fa]
[2023-03-15 07:08:30,042] [INFO] Query marker FASTA was written to OceanDNA-b31321/markers.fasta
[2023-03-15 07:08:30,043] [INFO] Task started: Blastn
[2023-03-15 07:08:30,043] [INFO] Running command: blastn -query OceanDNA-b31321/markers.fasta -db /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/reference_markers.fasta -out OceanDNA-b31321/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:08:30,521] [INFO] Task succeeded: Blastn
[2023-03-15 07:08:30,522] [INFO] Selected 5 target genomes.
[2023-03-15 07:08:30,522] [INFO] Target genome list was writen to OceanDNA-b31321/target_genomes.txt
[2023-03-15 07:08:30,525] [INFO] Task started: fastANI
[2023-03-15 07:08:30,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg0660236b-89f8-43b4-8bc4-defad5e75e21/OceanDNA-b31321.fa --refList OceanDNA-b31321/target_genomes.txt --output OceanDNA-b31321/fastani_result.tsv --threads 1
[2023-03-15 07:08:32,117] [INFO] Task succeeded: fastANI
[2023-03-15 07:08:32,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:08:32,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:08:32,117] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:08:32,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 07:08:32,118] [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 07:08:32,119] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31321/tc_result.tsv
[2023-03-15 07:08:32,119] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:08:32,120] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:08:32,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/checkm_data
[2023-03-15 07:08:32,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:08:32,177] [INFO] Task started: CheckM
[2023-03-15 07:08:32,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31321/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31321/checkm_input OceanDNA-b31321/checkm_result
[2023-03-15 07:08:48,583] [INFO] Task succeeded: CheckM
[2023-03-15 07:08:48,583] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.48%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:08:48,586] [INFO] ===== Completeness check finished =====
[2023-03-15 07:08:48,586] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:08:48,587] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31321/markers.fasta)
[2023-03-15 07:08:48,588] [INFO] Task started: Blastn
[2023-03-15 07:08:48,588] [INFO] Running command: blastn -query OceanDNA-b31321/markers.fasta -db /var/lib/cwl/stgbd81071c-694f-46c7-8aa7-bbebaacf5da4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31321/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:08:49,344] [INFO] Task succeeded: Blastn
[2023-03-15 07:08:49,346] [INFO] Selected 14 target genomes.
[2023-03-15 07:08:49,346] [INFO] Target genome list was writen to OceanDNA-b31321/target_genomes_gtdb.txt
[2023-03-15 07:08:49,382] [INFO] Task started: fastANI
[2023-03-15 07:08:49,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg0660236b-89f8-43b4-8bc4-defad5e75e21/OceanDNA-b31321.fa --refList OceanDNA-b31321/target_genomes_gtdb.txt --output OceanDNA-b31321/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:08:52,501] [INFO] Task succeeded: fastANI
[2023-03-15 07:08:52,503] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:08:52,503] [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_018667735.1	s__JABIRX01 sp018667735	99.8699	55	56	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__JABIRX01;g__JABIRX01	95.0	99.81	99.81	0.90	0.90	2	conclusive
--------------------------------------------------------------------------------
[2023-03-15 07:08:52,504] [INFO] GTDB search result was written to OceanDNA-b31321/result_gtdb.tsv
[2023-03-15 07:08:52,504] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:08:52,504] [INFO] DFAST_QC result json was written to OceanDNA-b31321/dqc_result.json
[2023-03-15 07:08:52,504] [INFO] DFAST_QC completed!
[2023-03-15 07:08:52,505] [INFO] Total running time: 0h0m26s