[2023-03-16 00:33:46,599] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference
[2023-03-16 00:33:47,716] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,716] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,717] [INFO] Running command: cat /var/lib/cwl/stgf4ae1330-3488-458c-b14c-c27e2db09ebb/OceanDNA-b24232.fa | prodigal -d OceanDNA-b24232/cds.fna -a OceanDNA-b24232/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:33:53,418] [INFO] Task succeeded: Prodigal
[2023-03-16 00:33:53,418] [INFO] Task started: HMMsearch
[2023-03-16 00:33:53,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b24232/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/reference_markers.hmm OceanDNA-b24232/protein.faa > /dev/null
[2023-03-16 00:33:53,577] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:33:53,578] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf4ae1330-3488-458c-b14c-c27e2db09ebb/OceanDNA-b24232.fa]
[2023-03-16 00:33:53,591] [INFO] Query marker FASTA was written to OceanDNA-b24232/markers.fasta
[2023-03-16 00:33:53,591] [INFO] Task started: Blastn
[2023-03-16 00:33:53,591] [INFO] Running command: blastn -query OceanDNA-b24232/markers.fasta -db /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/reference_markers.fasta -out OceanDNA-b24232/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:33:54,273] [INFO] Task succeeded: Blastn
[2023-03-16 00:33:54,273] [INFO] Selected 8 target genomes.
[2023-03-16 00:33:54,274] [INFO] Target genome list was writen to OceanDNA-b24232/target_genomes.txt
[2023-03-16 00:33:54,372] [INFO] Task started: fastANI
[2023-03-16 00:33:54,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ae1330-3488-458c-b14c-c27e2db09ebb/OceanDNA-b24232.fa --refList OceanDNA-b24232/target_genomes.txt --output OceanDNA-b24232/fastani_result.tsv --threads 1
[2023-03-16 00:33:58,113] [INFO] Task succeeded: fastANI
[2023-03-16 00:33:58,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:33:58,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:33:58,114] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:33:58,114] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:33:58,114] [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 00:33:58,114] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24232/tc_result.tsv
[2023-03-16 00:33:58,114] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:33:58,114] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:33:58,114] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/checkm_data
[2023-03-16 00:33:58,117] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:33:58,123] [INFO] Task started: CheckM
[2023-03-16 00:33:58,123] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24232/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24232/checkm_input OceanDNA-b24232/checkm_result
[2023-03-16 00:34:21,062] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:21,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.23%
Contamintation: 9.38%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-16 00:34:21,064] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:21,065] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:21,065] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24232/markers.fasta)
[2023-03-16 00:34:21,065] [INFO] Task started: Blastn
[2023-03-16 00:34:21,065] [INFO] Running command: blastn -query OceanDNA-b24232/markers.fasta -db /var/lib/cwl/stg5e94a1b2-f58f-4ec0-9103-54eaebf03199/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24232/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:21,675] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:21,676] [INFO] Selected 17 target genomes.
[2023-03-16 00:34:21,676] [INFO] Target genome list was writen to OceanDNA-b24232/target_genomes_gtdb.txt
[2023-03-16 00:34:21,855] [INFO] Task started: fastANI
[2023-03-16 00:34:21,855] [INFO] Running command: fastANI --query /var/lib/cwl/stgf4ae1330-3488-458c-b14c-c27e2db09ebb/OceanDNA-b24232.fa --refList OceanDNA-b24232/target_genomes_gtdb.txt --output OceanDNA-b24232/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:26,088] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:26,092] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 00:34:26,092] [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_002701885.1	s__GCA-2701885 sp002701885	99.5416	254	357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2701885;f__GCA-2701885;g__GCA-2701885	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722055.1	s__GCA-2701885 sp002722055	80.1973	209	357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2701885;f__GCA-2701885;g__GCA-2701885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938125.1	s__GCA-2701885 sp002938125	79.0062	167	357	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2701885;f__GCA-2701885;g__GCA-2701885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:34:26,092] [INFO] GTDB search result was written to OceanDNA-b24232/result_gtdb.tsv
[2023-03-16 00:34:26,092] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:26,093] [INFO] DFAST_QC result json was written to OceanDNA-b24232/dqc_result.json
[2023-03-16 00:34:26,093] [INFO] DFAST_QC completed!
[2023-03-16 00:34:26,093] [INFO] Total running time: 0h0m39s