[2023-03-14 13:55:26,704] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:55:26,704] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:55:26,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference
[2023-03-14 13:55:29,872] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:55:29,873] [INFO] Task started: Prodigal
[2023-03-14 13:55:29,874] [INFO] Running command: cat /var/lib/cwl/stg413f499c-4ae7-4876-b8bc-2a44200515b9/OceanDNA-b26126.fa | prodigal -d OceanDNA-b26126/cds.fna -a OceanDNA-b26126/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:55:42,484] [INFO] Task succeeded: Prodigal
[2023-03-14 13:55:42,485] [INFO] Task started: HMMsearch
[2023-03-14 13:55:42,485] [INFO] Running command: hmmsearch --tblout OceanDNA-b26126/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/reference_markers.hmm OceanDNA-b26126/protein.faa > /dev/null
[2023-03-14 13:55:42,742] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:55:42,743] [INFO] Found 6/6 markers.
[2023-03-14 13:55:42,777] [INFO] Query marker FASTA was written to OceanDNA-b26126/markers.fasta
[2023-03-14 13:55:42,779] [INFO] Task started: Blastn
[2023-03-14 13:55:42,779] [INFO] Running command: blastn -query OceanDNA-b26126/markers.fasta -db /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/reference_markers.fasta -out OceanDNA-b26126/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:55:43,445] [INFO] Task succeeded: Blastn
[2023-03-14 13:55:43,446] [INFO] Selected 27 target genomes.
[2023-03-14 13:55:43,446] [INFO] Target genome list was writen to OceanDNA-b26126/target_genomes.txt
[2023-03-14 13:55:43,467] [INFO] Task started: fastANI
[2023-03-14 13:55:43,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg413f499c-4ae7-4876-b8bc-2a44200515b9/OceanDNA-b26126.fa --refList OceanDNA-b26126/target_genomes.txt --output OceanDNA-b26126/fastani_result.tsv --threads 1
[2023-03-14 13:56:04,274] [INFO] Task succeeded: fastANI
[2023-03-14 13:56:04,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:56:04,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:56:04,274] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:56:04,274] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:56:04,275] [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
--------------------------------------------------------------------------------
[2023-03-14 13:56:04,275] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26126/tc_result.tsv
[2023-03-14 13:56:04,275] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:56:04,275] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:56:04,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/checkm_data
[2023-03-14 13:56:04,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:56:04,292] [INFO] Task started: CheckM
[2023-03-14 13:56:04,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26126/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26126/checkm_input OceanDNA-b26126/checkm_result
[2023-03-14 13:56:40,403] [INFO] Task succeeded: CheckM
[2023-03-14 13:56:40,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:56:40,406] [INFO] ===== Completeness check finished =====
[2023-03-14 13:56:40,406] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:56:40,406] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26126/markers.fasta)
[2023-03-14 13:56:40,407] [INFO] Task started: Blastn
[2023-03-14 13:56:40,407] [INFO] Running command: blastn -query OceanDNA-b26126/markers.fasta -db /var/lib/cwl/stg2e22ee5c-a23c-4813-851e-a7da8128548b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26126/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:56:41,380] [INFO] Task succeeded: Blastn
[2023-03-14 13:56:41,381] [INFO] Selected 21 target genomes.
[2023-03-14 13:56:41,381] [INFO] Target genome list was writen to OceanDNA-b26126/target_genomes_gtdb.txt
[2023-03-14 13:56:41,391] [INFO] Task started: fastANI
[2023-03-14 13:56:41,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg413f499c-4ae7-4876-b8bc-2a44200515b9/OceanDNA-b26126.fa --refList OceanDNA-b26126/target_genomes_gtdb.txt --output OceanDNA-b26126/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:56:48,983] [INFO] Task succeeded: fastANI
[2023-03-14 13:56:48,987] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:56:48,987] [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_011524805.1	s__WTJO01 sp011524805	98.408	409	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__WTJO01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000238815.2	s__HIMB100 sp000238815	76.6626	94	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__HIMB100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780775.1	s__JADHLI01 sp016780775	76.4749	75	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__JADHLI01	95.0	99.93	99.93	0.97	0.97	2	-
GCA_002387605.1	s__UBA4588 sp002387605	76.234	68	488	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA4588	95.0	99.40	98.72	0.91	0.85	18	-
--------------------------------------------------------------------------------
[2023-03-14 13:56:48,987] [INFO] GTDB search result was written to OceanDNA-b26126/result_gtdb.tsv
[2023-03-14 13:56:48,987] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:56:48,988] [INFO] DFAST_QC result json was written to OceanDNA-b26126/dqc_result.json
[2023-03-14 13:56:48,988] [INFO] DFAST_QC completed!
[2023-03-14 13:56:48,988] [INFO] Total running time: 0h1m22s