[2023-03-16 03:23:48,507] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:48,507] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:48,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference
[2023-03-16 03:23:50,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:50,644] [INFO] Task started: Prodigal
[2023-03-16 03:23:50,644] [INFO] Running command: cat /var/lib/cwl/stgb9ed8eee-0665-48fa-a9cd-8eb41fbac70e/OceanDNA-b28259.fa | prodigal -d OceanDNA-b28259/cds.fna -a OceanDNA-b28259/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:57,232] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:57,233] [INFO] Task started: HMMsearch
[2023-03-16 03:23:57,233] [INFO] Running command: hmmsearch --tblout OceanDNA-b28259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/reference_markers.hmm OceanDNA-b28259/protein.faa > /dev/null
[2023-03-16 03:23:57,427] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:57,427] [INFO] Found 6/6 markers.
[2023-03-16 03:23:57,440] [INFO] Query marker FASTA was written to OceanDNA-b28259/markers.fasta
[2023-03-16 03:23:57,440] [INFO] Task started: Blastn
[2023-03-16 03:23:57,440] [INFO] Running command: blastn -query OceanDNA-b28259/markers.fasta -db /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/reference_markers.fasta -out OceanDNA-b28259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:57,961] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:57,962] [INFO] Selected 10 target genomes.
[2023-03-16 03:23:57,962] [INFO] Target genome list was writen to OceanDNA-b28259/target_genomes.txt
[2023-03-16 03:23:57,968] [INFO] Task started: fastANI
[2023-03-16 03:23:57,969] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ed8eee-0665-48fa-a9cd-8eb41fbac70e/OceanDNA-b28259.fa --refList OceanDNA-b28259/target_genomes.txt --output OceanDNA-b28259/fastani_result.tsv --threads 1
[2023-03-16 03:24:02,872] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:02,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:02,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:02,873] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:02,873] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 03:24:02,873] [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 03:24:02,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28259/tc_result.tsv
[2023-03-16 03:24:02,873] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:02,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:02,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/checkm_data
[2023-03-16 03:24:02,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:02,879] [INFO] Task started: CheckM
[2023-03-16 03:24:02,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28259/checkm_input OceanDNA-b28259/checkm_result
[2023-03-16 03:24:25,391] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:25,391] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.66%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:25,393] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:25,393] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:25,393] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28259/markers.fasta)
[2023-03-16 03:24:25,394] [INFO] Task started: Blastn
[2023-03-16 03:24:25,394] [INFO] Running command: blastn -query OceanDNA-b28259/markers.fasta -db /var/lib/cwl/stg9bc3e296-213a-4fbb-8b09-0e5fb07984f0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:26,090] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:26,091] [INFO] Selected 26 target genomes.
[2023-03-16 03:24:26,091] [INFO] Target genome list was writen to OceanDNA-b28259/target_genomes_gtdb.txt
[2023-03-16 03:24:26,893] [INFO] Task started: fastANI
[2023-03-16 03:24:26,893] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9ed8eee-0665-48fa-a9cd-8eb41fbac70e/OceanDNA-b28259.fa --refList OceanDNA-b28259/target_genomes_gtdb.txt --output OceanDNA-b28259/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:33,901] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:33,905] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:33,905] [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_902599445.1	s__CACIIZ01 sp902599445	93.5877	242	402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699695.2	s__CACIIZ01 sp002699695	80.036	199	402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902586855.1	s__CACIIZ01 sp902586855	79.7193	92	402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239455.1	s__CACIIZ01 sp014239455	79.7172	101	402	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CACIIZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:33,905] [INFO] GTDB search result was written to OceanDNA-b28259/result_gtdb.tsv
[2023-03-16 03:24:33,905] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:33,906] [INFO] DFAST_QC result json was written to OceanDNA-b28259/dqc_result.json
[2023-03-16 03:24:33,906] [INFO] DFAST_QC completed!
[2023-03-16 03:24:33,906] [INFO] Total running time: 0h0m45s