[2023-03-17 23:08:31,927] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,927] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,927] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference
[2023-03-17 23:08:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,079] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,080] [INFO] Running command: cat /var/lib/cwl/stgba3c9d1f-04e2-456b-b72a-42f6e10381ff/OceanDNA-b13178.fa | prodigal -d OceanDNA-b13178/cds.fna -a OceanDNA-b13178/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:54,414] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:54,414] [INFO] Task started: HMMsearch
[2023-03-17 23:08:54,414] [INFO] Running command: hmmsearch --tblout OceanDNA-b13178/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/reference_markers.hmm OceanDNA-b13178/protein.faa > /dev/null
[2023-03-17 23:08:54,649] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:54,650] [INFO] Found 6/6 markers.
[2023-03-17 23:08:54,677] [INFO] Query marker FASTA was written to OceanDNA-b13178/markers.fasta
[2023-03-17 23:08:54,677] [INFO] Task started: Blastn
[2023-03-17 23:08:54,678] [INFO] Running command: blastn -query OceanDNA-b13178/markers.fasta -db /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/reference_markers.fasta -out OceanDNA-b13178/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:55,188] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:55,188] [INFO] Selected 23 target genomes.
[2023-03-17 23:08:55,189] [INFO] Target genome list was writen to OceanDNA-b13178/target_genomes.txt
[2023-03-17 23:08:55,201] [INFO] Task started: fastANI
[2023-03-17 23:08:55,201] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3c9d1f-04e2-456b-b72a-42f6e10381ff/OceanDNA-b13178.fa --refList OceanDNA-b13178/target_genomes.txt --output OceanDNA-b13178/fastani_result.tsv --threads 1
[2023-03-17 23:09:07,851] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:07,851] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:07,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:07,852] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:07,852] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:09:07,852] [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 23:09:07,854] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13178/tc_result.tsv
[2023-03-17 23:09:07,861] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:07,861] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:07,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/checkm_data
[2023-03-17 23:09:07,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:07,871] [INFO] Task started: CheckM
[2023-03-17 23:09:07,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13178/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13178/checkm_input OceanDNA-b13178/checkm_result
[2023-03-17 23:10:01,698] [INFO] Task succeeded: CheckM
[2023-03-17 23:10:01,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:10:01,717] [INFO] ===== Completeness check finished =====
[2023-03-17 23:10:01,717] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:10:01,717] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13178/markers.fasta)
[2023-03-17 23:10:01,718] [INFO] Task started: Blastn
[2023-03-17 23:10:01,718] [INFO] Running command: blastn -query OceanDNA-b13178/markers.fasta -db /var/lib/cwl/stg4a678496-9cb1-46cb-b9c7-e48ad3c06ca9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13178/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:10:02,456] [INFO] Task succeeded: Blastn
[2023-03-17 23:10:02,461] [INFO] Selected 18 target genomes.
[2023-03-17 23:10:02,461] [INFO] Target genome list was writen to OceanDNA-b13178/target_genomes_gtdb.txt
[2023-03-17 23:10:02,475] [INFO] Task started: fastANI
[2023-03-17 23:10:02,475] [INFO] Running command: fastANI --query /var/lib/cwl/stgba3c9d1f-04e2-456b-b72a-42f6e10381ff/OceanDNA-b13178.fa --refList OceanDNA-b13178/target_genomes_gtdb.txt --output OceanDNA-b13178/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:10:11,818] [INFO] Task succeeded: fastANI
[2023-03-17 23:10:11,820] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:10:11,821] [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_002474345.1	s__UBA7317 sp002474345	99.5994	1098	1385	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA7317	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002715375.1	s__UBA7317 sp002715375	82.736	613	1385	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__UBA7317	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:10:11,823] [INFO] GTDB search result was written to OceanDNA-b13178/result_gtdb.tsv
[2023-03-17 23:10:11,827] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:10:11,830] [INFO] DFAST_QC result json was written to OceanDNA-b13178/dqc_result.json
[2023-03-17 23:10:11,830] [INFO] DFAST_QC completed!
[2023-03-17 23:10:11,830] [INFO] Total running time: 0h1m40s