[2023-03-19 04:55:39,425] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,425] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,425] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stg2aac5005-79c8-4a2e-b795-ee1e3d80c126/OceanDNA-b45264.fa | prodigal -d OceanDNA-b45264/cds.fna -a OceanDNA-b45264/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:55:48,793] [INFO] Task succeeded: Prodigal
[2023-03-19 04:55:48,794] [INFO] Task started: HMMsearch
[2023-03-19 04:55:48,794] [INFO] Running command: hmmsearch --tblout OceanDNA-b45264/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/reference_markers.hmm OceanDNA-b45264/protein.faa > /dev/null
[2023-03-19 04:55:48,941] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:55:48,942] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2aac5005-79c8-4a2e-b795-ee1e3d80c126/OceanDNA-b45264.fa]
[2023-03-19 04:55:48,970] [INFO] Query marker FASTA was written to OceanDNA-b45264/markers.fasta
[2023-03-19 04:55:48,970] [INFO] Task started: Blastn
[2023-03-19 04:55:48,970] [INFO] Running command: blastn -query OceanDNA-b45264/markers.fasta -db /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/reference_markers.fasta -out OceanDNA-b45264/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:55:49,508] [INFO] Task succeeded: Blastn
[2023-03-19 04:55:49,514] [INFO] Selected 21 target genomes.
[2023-03-19 04:55:49,514] [INFO] Target genome list was writen to OceanDNA-b45264/target_genomes.txt
[2023-03-19 04:55:49,530] [INFO] Task started: fastANI
[2023-03-19 04:55:49,531] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aac5005-79c8-4a2e-b795-ee1e3d80c126/OceanDNA-b45264.fa --refList OceanDNA-b45264/target_genomes.txt --output OceanDNA-b45264/fastani_result.tsv --threads 1
[2023-03-19 04:56:02,693] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:02,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:56:02,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:56:02,693] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:56:02,694] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:56:02,694] [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
--------------------------------------------------------------------------------
[2023-03-19 04:56:02,768] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45264/tc_result.tsv
[2023-03-19 04:56:02,769] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:56:02,769] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:56:02,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/checkm_data
[2023-03-19 04:56:02,772] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:56:02,782] [INFO] Task started: CheckM
[2023-03-19 04:56:02,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45264/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45264/checkm_input OceanDNA-b45264/checkm_result
[2023-03-19 04:56:28,465] [INFO] Task succeeded: CheckM
[2023-03-19 04:56:28,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.86%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-19 04:56:28,481] [INFO] ===== Completeness check finished =====
[2023-03-19 04:56:28,481] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:56:28,482] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45264/markers.fasta)
[2023-03-19 04:56:28,482] [INFO] Task started: Blastn
[2023-03-19 04:56:28,482] [INFO] Running command: blastn -query OceanDNA-b45264/markers.fasta -db /var/lib/cwl/stg2a50040d-e09a-4836-9701-d74fe0d59bc5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45264/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:29,231] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:29,235] [INFO] Selected 22 target genomes.
[2023-03-19 04:56:29,236] [INFO] Target genome list was writen to OceanDNA-b45264/target_genomes_gtdb.txt
[2023-03-19 04:56:29,252] [INFO] Task started: fastANI
[2023-03-19 04:56:29,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg2aac5005-79c8-4a2e-b795-ee1e3d80c126/OceanDNA-b45264.fa --refList OceanDNA-b45264/target_genomes_gtdb.txt --output OceanDNA-b45264/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:56:40,067] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:40,069] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:56:40,069] [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_016190025.1	s__JACPRG01 sp016190025	78.0624	83	271	d__Bacteria;p__UBA8248;c__UBA8248;o__JACPRG01;f__JACPRG01;g__JACPRG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:56:40,074] [INFO] GTDB search result was written to OceanDNA-b45264/result_gtdb.tsv
[2023-03-19 04:56:40,079] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:56:40,085] [INFO] DFAST_QC result json was written to OceanDNA-b45264/dqc_result.json
[2023-03-19 04:56:40,085] [INFO] DFAST_QC completed!
[2023-03-19 04:56:40,085] [INFO] Total running time: 0h1m1s