[2023-03-16 03:47:34,636] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:34,636] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:34,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference
[2023-03-16 03:47:35,754] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:35,754] [INFO] Task started: Prodigal
[2023-03-16 03:47:35,754] [INFO] Running command: cat /var/lib/cwl/stgcfeb2e98-1567-439f-b519-f983a6b558b9/OceanDNA-b26827.fa | prodigal -d OceanDNA-b26827/cds.fna -a OceanDNA-b26827/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:43,616] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:43,617] [INFO] Task started: HMMsearch
[2023-03-16 03:47:43,617] [INFO] Running command: hmmsearch --tblout OceanDNA-b26827/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/reference_markers.hmm OceanDNA-b26827/protein.faa > /dev/null
[2023-03-16 03:47:43,867] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:43,868] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfeb2e98-1567-439f-b519-f983a6b558b9/OceanDNA-b26827.fa]
[2023-03-16 03:47:43,886] [INFO] Query marker FASTA was written to OceanDNA-b26827/markers.fasta
[2023-03-16 03:47:43,886] [INFO] Task started: Blastn
[2023-03-16 03:47:43,886] [INFO] Running command: blastn -query OceanDNA-b26827/markers.fasta -db /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/reference_markers.fasta -out OceanDNA-b26827/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:44,373] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:44,373] [INFO] Selected 13 target genomes.
[2023-03-16 03:47:44,374] [INFO] Target genome list was writen to OceanDNA-b26827/target_genomes.txt
[2023-03-16 03:47:44,381] [INFO] Task started: fastANI
[2023-03-16 03:47:44,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfeb2e98-1567-439f-b519-f983a6b558b9/OceanDNA-b26827.fa --refList OceanDNA-b26827/target_genomes.txt --output OceanDNA-b26827/fastani_result.tsv --threads 1
[2023-03-16 03:47:52,809] [INFO] Task succeeded: fastANI
[2023-03-16 03:47:52,810] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:47:52,810] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:47:52,810] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:47:52,810] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:47:52,810] [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
--------------------------------------------------------------------------------
[2023-03-16 03:47:52,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26827/tc_result.tsv
[2023-03-16 03:47:52,810] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:47:52,811] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:47:52,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/checkm_data
[2023-03-16 03:47:52,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:47:52,817] [INFO] Task started: CheckM
[2023-03-16 03:47:52,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26827/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26827/checkm_input OceanDNA-b26827/checkm_result
[2023-03-16 03:48:19,080] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:19,081] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:19,083] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:19,083] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:19,083] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26827/markers.fasta)
[2023-03-16 03:48:19,084] [INFO] Task started: Blastn
[2023-03-16 03:48:19,084] [INFO] Running command: blastn -query OceanDNA-b26827/markers.fasta -db /var/lib/cwl/stgab176a74-ecd2-4c0e-bf46-e1422ef5b8e3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26827/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:19,690] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:19,691] [INFO] Selected 16 target genomes.
[2023-03-16 03:48:19,691] [INFO] Target genome list was writen to OceanDNA-b26827/target_genomes_gtdb.txt
[2023-03-16 03:48:19,705] [INFO] Task started: fastANI
[2023-03-16 03:48:19,705] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfeb2e98-1567-439f-b519-f983a6b558b9/OceanDNA-b26827.fa --refList OceanDNA-b26827/target_genomes_gtdb.txt --output OceanDNA-b26827/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:48:29,326] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:29,327] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:48:29,327] [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
--------------------------------------------------------------------------------
[2023-03-16 03:48:29,327] [INFO] GTDB search result was written to OceanDNA-b26827/result_gtdb.tsv
[2023-03-16 03:48:29,327] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:48:29,327] [INFO] DFAST_QC result json was written to OceanDNA-b26827/dqc_result.json
[2023-03-16 03:48:29,327] [INFO] DFAST_QC completed!
[2023-03-16 03:48:29,327] [INFO] Total running time: 0h0m55s