[2023-03-15 03:25:37,034] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,034] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference
[2023-03-15 03:25:38,117] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,118] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,118] [INFO] Running command: cat /var/lib/cwl/stg3f465cd5-6d5c-466e-9d77-36b63b76c9b1/OceanDNA-b44053.fa | prodigal -d OceanDNA-b44053/cds.fna -a OceanDNA-b44053/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:25:49,989] [INFO] Task succeeded: Prodigal
[2023-03-15 03:25:49,989] [INFO] Task started: HMMsearch
[2023-03-15 03:25:49,989] [INFO] Running command: hmmsearch --tblout OceanDNA-b44053/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/reference_markers.hmm OceanDNA-b44053/protein.faa > /dev/null
[2023-03-15 03:25:50,175] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:25:50,175] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f465cd5-6d5c-466e-9d77-36b63b76c9b1/OceanDNA-b44053.fa]
[2023-03-15 03:25:50,198] [INFO] Query marker FASTA was written to OceanDNA-b44053/markers.fasta
[2023-03-15 03:25:50,199] [INFO] Task started: Blastn
[2023-03-15 03:25:50,199] [INFO] Running command: blastn -query OceanDNA-b44053/markers.fasta -db /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/reference_markers.fasta -out OceanDNA-b44053/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:25:50,774] [INFO] Task succeeded: Blastn
[2023-03-15 03:25:50,776] [INFO] Selected 30 target genomes.
[2023-03-15 03:25:50,776] [INFO] Target genome list was writen to OceanDNA-b44053/target_genomes.txt
[2023-03-15 03:25:50,793] [INFO] Task started: fastANI
[2023-03-15 03:25:50,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f465cd5-6d5c-466e-9d77-36b63b76c9b1/OceanDNA-b44053.fa --refList OceanDNA-b44053/target_genomes.txt --output OceanDNA-b44053/fastani_result.tsv --threads 1
[2023-03-15 03:26:08,821] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:08,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:08,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:08,822] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:08,822] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:26:08,822] [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 03:26:08,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44053/tc_result.tsv
[2023-03-15 03:26:08,822] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:08,822] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:08,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/checkm_data
[2023-03-15 03:26:08,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:08,829] [INFO] Task started: CheckM
[2023-03-15 03:26:08,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44053/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44053/checkm_input OceanDNA-b44053/checkm_result
[2023-03-15 03:26:43,197] [INFO] Task succeeded: CheckM
[2023-03-15 03:26:43,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.80%
Contamintation: 10.77%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-15 03:26:43,200] [INFO] ===== Completeness check finished =====
[2023-03-15 03:26:43,200] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:26:43,200] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44053/markers.fasta)
[2023-03-15 03:26:43,201] [INFO] Task started: Blastn
[2023-03-15 03:26:43,201] [INFO] Running command: blastn -query OceanDNA-b44053/markers.fasta -db /var/lib/cwl/stg30f289e2-16b0-49be-ae64-14391700f4ee/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44053/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:44,109] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:44,111] [INFO] Selected 29 target genomes.
[2023-03-15 03:26:44,111] [INFO] Target genome list was writen to OceanDNA-b44053/target_genomes_gtdb.txt
[2023-03-15 03:26:44,159] [INFO] Task started: fastANI
[2023-03-15 03:26:44,160] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f465cd5-6d5c-466e-9d77-36b63b76c9b1/OceanDNA-b44053.fa --refList OceanDNA-b44053/target_genomes_gtdb.txt --output OceanDNA-b44053/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:26:58,798] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:58,800] [INFO] Found 1 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:26:58,800] [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_012103475.1	s__WLWS01 sp012103475	77.0557	123	581	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA4486;f__UBA4486;g__WLWS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:26:58,800] [INFO] GTDB search result was written to OceanDNA-b44053/result_gtdb.tsv
[2023-03-15 03:26:58,800] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:26:58,800] [INFO] DFAST_QC result json was written to OceanDNA-b44053/dqc_result.json
[2023-03-15 03:26:58,801] [INFO] DFAST_QC completed!
[2023-03-15 03:26:58,801] [INFO] Total running time: 0h1m22s