[2023-03-17 07:28:31,298] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,298] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference
[2023-03-17 07:28:33,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stgcd1a1aea-e814-4f2a-8ccd-e7278932367a/OceanDNA-b34143.fa | prodigal -d OceanDNA-b34143/cds.fna -a OceanDNA-b34143/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:40,907] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:40,908] [INFO] Task started: HMMsearch
[2023-03-17 07:28:40,908] [INFO] Running command: hmmsearch --tblout OceanDNA-b34143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/reference_markers.hmm OceanDNA-b34143/protein.faa > /dev/null
[2023-03-17 07:28:41,116] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:41,117] [INFO] Found 6/6 markers.
[2023-03-17 07:28:41,131] [INFO] Query marker FASTA was written to OceanDNA-b34143/markers.fasta
[2023-03-17 07:28:41,131] [INFO] Task started: Blastn
[2023-03-17 07:28:41,131] [INFO] Running command: blastn -query OceanDNA-b34143/markers.fasta -db /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/reference_markers.fasta -out OceanDNA-b34143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:41,655] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:41,656] [INFO] Selected 15 target genomes.
[2023-03-17 07:28:41,656] [INFO] Target genome list was writen to OceanDNA-b34143/target_genomes.txt
[2023-03-17 07:28:41,664] [INFO] Task started: fastANI
[2023-03-17 07:28:41,664] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1a1aea-e814-4f2a-8ccd-e7278932367a/OceanDNA-b34143.fa --refList OceanDNA-b34143/target_genomes.txt --output OceanDNA-b34143/fastani_result.tsv --threads 1
[2023-03-17 07:28:47,916] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:47,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:47,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:47,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:47,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:47,917] [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 07:28:47,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34143/tc_result.tsv
[2023-03-17 07:28:47,917] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:47,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:47,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/checkm_data
[2023-03-17 07:28:47,920] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:47,924] [INFO] Task started: CheckM
[2023-03-17 07:28:47,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34143/checkm_input OceanDNA-b34143/checkm_result
[2023-03-17 07:29:12,646] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:12,646] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:12,648] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:12,648] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:12,649] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34143/markers.fasta)
[2023-03-17 07:29:12,649] [INFO] Task started: Blastn
[2023-03-17 07:29:12,649] [INFO] Running command: blastn -query OceanDNA-b34143/markers.fasta -db /var/lib/cwl/stg3854f5f4-8502-49f9-88b8-8d801c43e6c5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:13,459] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:13,460] [INFO] Selected 27 target genomes.
[2023-03-17 07:29:13,460] [INFO] Target genome list was writen to OceanDNA-b34143/target_genomes_gtdb.txt
[2023-03-17 07:29:14,001] [INFO] Task started: fastANI
[2023-03-17 07:29:14,002] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1a1aea-e814-4f2a-8ccd-e7278932367a/OceanDNA-b34143.fa --refList OceanDNA-b34143/target_genomes_gtdb.txt --output OceanDNA-b34143/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:22,578] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:22,580] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:22,580] [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_002704665.1	s__GCA-2704665 sp002704665	99.9212	356	456	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__UBA3031;g__GCA-2704665	95.0	N/A	N/A	N/A	N/A	1	conclusive
--------------------------------------------------------------------------------
[2023-03-17 07:29:22,580] [INFO] GTDB search result was written to OceanDNA-b34143/result_gtdb.tsv
[2023-03-17 07:29:22,580] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:22,581] [INFO] DFAST_QC result json was written to OceanDNA-b34143/dqc_result.json
[2023-03-17 07:29:22,581] [INFO] DFAST_QC completed!
[2023-03-17 07:29:22,581] [INFO] Total running time: 0h0m51s