[2023-03-15 08:25:09,336] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:25:09,337] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:25:09,337] [INFO] DQC Reference Directory: /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference
[2023-03-15 08:25:10,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:25:10,456] [INFO] Task started: Prodigal
[2023-03-15 08:25:10,456] [INFO] Running command: cat /var/lib/cwl/stg8a241b3f-c3e9-4e3e-be3b-4d917a94ea44/OceanDNA-b28332.fa | prodigal -d OceanDNA-b28332/cds.fna -a OceanDNA-b28332/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:25:20,805] [INFO] Task succeeded: Prodigal
[2023-03-15 08:25:20,806] [INFO] Task started: HMMsearch
[2023-03-15 08:25:20,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b28332/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/reference_markers.hmm OceanDNA-b28332/protein.faa > /dev/null
[2023-03-15 08:25:20,980] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:25:20,981] [INFO] Found 6/6 markers.
[2023-03-15 08:25:20,998] [INFO] Query marker FASTA was written to OceanDNA-b28332/markers.fasta
[2023-03-15 08:25:21,000] [INFO] Task started: Blastn
[2023-03-15 08:25:21,000] [INFO] Running command: blastn -query OceanDNA-b28332/markers.fasta -db /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/reference_markers.fasta -out OceanDNA-b28332/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:25:21,561] [INFO] Task succeeded: Blastn
[2023-03-15 08:25:21,563] [INFO] Selected 24 target genomes.
[2023-03-15 08:25:21,563] [INFO] Target genome list was writen to OceanDNA-b28332/target_genomes.txt
[2023-03-15 08:25:21,576] [INFO] Task started: fastANI
[2023-03-15 08:25:21,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a241b3f-c3e9-4e3e-be3b-4d917a94ea44/OceanDNA-b28332.fa --refList OceanDNA-b28332/target_genomes.txt --output OceanDNA-b28332/fastani_result.tsv --threads 1
[2023-03-15 08:25:31,583] [INFO] Task succeeded: fastANI
[2023-03-15 08:25:31,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:25:31,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:25:31,583] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:25:31,584] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 08:25:31,584] [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 08:25:31,584] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28332/tc_result.tsv
[2023-03-15 08:25:31,585] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:25:31,585] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:25:31,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/checkm_data
[2023-03-15 08:25:31,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:25:31,592] [INFO] Task started: CheckM
[2023-03-15 08:25:31,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28332/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28332/checkm_input OceanDNA-b28332/checkm_result
[2023-03-15 08:26:01,626] [INFO] Task succeeded: CheckM
[2023-03-15 08:26:01,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.84%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 08:26:01,631] [INFO] ===== Completeness check finished =====
[2023-03-15 08:26:01,631] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:26:01,632] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28332/markers.fasta)
[2023-03-15 08:26:01,632] [INFO] Task started: Blastn
[2023-03-15 08:26:01,633] [INFO] Running command: blastn -query OceanDNA-b28332/markers.fasta -db /var/lib/cwl/stg2acdd4c1-cbb1-4e38-9ff9-e327b4df59c9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28332/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:26:02,599] [INFO] Task succeeded: Blastn
[2023-03-15 08:26:02,601] [INFO] Selected 29 target genomes.
[2023-03-15 08:26:02,601] [INFO] Target genome list was writen to OceanDNA-b28332/target_genomes_gtdb.txt
[2023-03-15 08:26:02,618] [INFO] Task started: fastANI
[2023-03-15 08:26:02,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a241b3f-c3e9-4e3e-be3b-4d917a94ea44/OceanDNA-b28332.fa --refList OceanDNA-b28332/target_genomes_gtdb.txt --output OceanDNA-b28332/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:26:12,614] [INFO] Task succeeded: fastANI
[2023-03-15 08:26:12,617] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:26:12,617] [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_905182165.1	s__GCA-002712045 sp905182165	96.9246	493	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-002712045	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002683355.1	s__GCA-002712045 sp002683355	78.4904	234	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-002712045	95.0	97.70	97.13	0.78	0.71	3	-
GCA_002712045.1	s__GCA-002712045 sp002712045	76.7324	148	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GCA-002712045	95.0	96.83	95.42	0.85	0.80	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:26:12,618] [INFO] GTDB search result was written to OceanDNA-b28332/result_gtdb.tsv
[2023-03-15 08:26:12,619] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:26:12,620] [INFO] DFAST_QC result json was written to OceanDNA-b28332/dqc_result.json
[2023-03-15 08:26:12,621] [INFO] DFAST_QC completed!
[2023-03-15 08:26:12,621] [INFO] Total running time: 0h1m3s