[2023-03-17 16:38:19,361] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:38:19,361] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:38:19,361] [INFO] DQC Reference Directory: /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference
[2023-03-17 16:38:21,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:38:21,575] [INFO] Task started: Prodigal
[2023-03-17 16:38:21,575] [INFO] Running command: cat /var/lib/cwl/stgfab51ee8-0c77-4578-a33a-358362dd66eb/OceanDNA-b21473.fa | prodigal -d OceanDNA-b21473/cds.fna -a OceanDNA-b21473/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:38:28,042] [INFO] Task succeeded: Prodigal
[2023-03-17 16:38:28,043] [INFO] Task started: HMMsearch
[2023-03-17 16:38:28,043] [INFO] Running command: hmmsearch --tblout OceanDNA-b21473/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/reference_markers.hmm OceanDNA-b21473/protein.faa > /dev/null
[2023-03-17 16:38:28,207] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:38:28,207] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfab51ee8-0c77-4578-a33a-358362dd66eb/OceanDNA-b21473.fa]
[2023-03-17 16:38:28,214] [INFO] Query marker FASTA was written to OceanDNA-b21473/markers.fasta
[2023-03-17 16:38:28,215] [INFO] Task started: Blastn
[2023-03-17 16:38:28,215] [INFO] Running command: blastn -query OceanDNA-b21473/markers.fasta -db /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/reference_markers.fasta -out OceanDNA-b21473/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:38:29,184] [INFO] Task succeeded: Blastn
[2023-03-17 16:38:29,185] [INFO] Selected 15 target genomes.
[2023-03-17 16:38:29,185] [INFO] Target genome list was writen to OceanDNA-b21473/target_genomes.txt
[2023-03-17 16:38:29,231] [INFO] Task started: fastANI
[2023-03-17 16:38:29,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab51ee8-0c77-4578-a33a-358362dd66eb/OceanDNA-b21473.fa --refList OceanDNA-b21473/target_genomes.txt --output OceanDNA-b21473/fastani_result.tsv --threads 1
[2023-03-17 16:38:40,362] [INFO] Task succeeded: fastANI
[2023-03-17 16:38:40,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:38:40,362] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:38:40,362] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:38:40,362] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 16:38:40,363] [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
--------------------------------------------------------------------------------
[2023-03-17 16:38:40,363] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21473/tc_result.tsv
[2023-03-17 16:38:40,363] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:38:40,363] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:38:40,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/checkm_data
[2023-03-17 16:38:40,419] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:38:40,424] [INFO] Task started: CheckM
[2023-03-17 16:38:40,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21473/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21473/checkm_input OceanDNA-b21473/checkm_result
[2023-03-17 16:39:06,698] [INFO] Task succeeded: CheckM
[2023-03-17 16:39:06,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 16:39:06,700] [INFO] ===== Completeness check finished =====
[2023-03-17 16:39:06,701] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:39:06,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21473/markers.fasta)
[2023-03-17 16:39:06,703] [INFO] Task started: Blastn
[2023-03-17 16:39:06,703] [INFO] Running command: blastn -query OceanDNA-b21473/markers.fasta -db /var/lib/cwl/stgeafc7ca8-687c-4983-a5e9-1df8cda92f88/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21473/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:39:07,911] [INFO] Task succeeded: Blastn
[2023-03-17 16:39:07,912] [INFO] Selected 17 target genomes.
[2023-03-17 16:39:07,912] [INFO] Target genome list was writen to OceanDNA-b21473/target_genomes_gtdb.txt
[2023-03-17 16:39:08,635] [INFO] Task started: fastANI
[2023-03-17 16:39:08,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab51ee8-0c77-4578-a33a-358362dd66eb/OceanDNA-b21473.fa --refList OceanDNA-b21473/target_genomes_gtdb.txt --output OceanDNA-b21473/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:39:12,802] [INFO] Task succeeded: fastANI
[2023-03-17 16:39:12,805] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 16:39:12,805] [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_002869235.1	s__BM519 sp002869235	78.7385	104	187	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__BM519	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599205.1	s__BM519 sp003599205	78.0502	68	187	d__Bacteria;p__Patescibacteria;c__ABY1;o__UBA1558;f__GWA2-36-10;g__BM519	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 16:39:12,805] [INFO] GTDB search result was written to OceanDNA-b21473/result_gtdb.tsv
[2023-03-17 16:39:12,805] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:39:12,805] [INFO] DFAST_QC result json was written to OceanDNA-b21473/dqc_result.json
[2023-03-17 16:39:12,806] [INFO] DFAST_QC completed!
[2023-03-17 16:39:12,806] [INFO] Total running time: 0h0m53s