[2023-03-17 23:08:31,965] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,965] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,965] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference
[2023-03-17 23:08:33,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,136] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,136] [INFO] Running command: cat /var/lib/cwl/stgdcb531b5-a20b-4b95-95c1-c99130f2e9af/OceanDNA-b32650.fa | prodigal -d OceanDNA-b32650/cds.fna -a OceanDNA-b32650/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:48,563] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:48,564] [INFO] Task started: HMMsearch
[2023-03-17 23:08:48,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b32650/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/reference_markers.hmm OceanDNA-b32650/protein.faa > /dev/null
[2023-03-17 23:08:48,862] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:48,863] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdcb531b5-a20b-4b95-95c1-c99130f2e9af/OceanDNA-b32650.fa]
[2023-03-17 23:08:48,906] [INFO] Query marker FASTA was written to OceanDNA-b32650/markers.fasta
[2023-03-17 23:08:48,907] [INFO] Task started: Blastn
[2023-03-17 23:08:48,907] [INFO] Running command: blastn -query OceanDNA-b32650/markers.fasta -db /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/reference_markers.fasta -out OceanDNA-b32650/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:49,449] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:49,453] [INFO] Selected 16 target genomes.
[2023-03-17 23:08:49,454] [INFO] Target genome list was writen to OceanDNA-b32650/target_genomes.txt
[2023-03-17 23:08:49,462] [INFO] Task started: fastANI
[2023-03-17 23:08:49,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcb531b5-a20b-4b95-95c1-c99130f2e9af/OceanDNA-b32650.fa --refList OceanDNA-b32650/target_genomes.txt --output OceanDNA-b32650/fastani_result.tsv --threads 1
[2023-03-17 23:09:00,136] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:00,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:09:00,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:09:00,136] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:09:00,136] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:09:00,137] [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 23:09:00,138] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32650/tc_result.tsv
[2023-03-17 23:09:00,139] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:09:00,139] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:09:00,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/checkm_data
[2023-03-17 23:09:00,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:09:00,151] [INFO] Task started: CheckM
[2023-03-17 23:09:00,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32650/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32650/checkm_input OceanDNA-b32650/checkm_result
[2023-03-17 23:09:43,969] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:43,970] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:44,014] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:44,014] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:44,015] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32650/markers.fasta)
[2023-03-17 23:09:44,016] [INFO] Task started: Blastn
[2023-03-17 23:09:44,016] [INFO] Running command: blastn -query OceanDNA-b32650/markers.fasta -db /var/lib/cwl/stgcd70a937-c77b-410f-b8e0-bff64d2e2cf4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32650/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:44,687] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:44,690] [INFO] Selected 13 target genomes.
[2023-03-17 23:09:44,690] [INFO] Target genome list was writen to OceanDNA-b32650/target_genomes_gtdb.txt
[2023-03-17 23:09:44,703] [INFO] Task started: fastANI
[2023-03-17 23:09:44,703] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcb531b5-a20b-4b95-95c1-c99130f2e9af/OceanDNA-b32650.fa --refList OceanDNA-b32650/target_genomes_gtdb.txt --output OceanDNA-b32650/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:53,623] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:53,625] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:09:53,625] [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_018650465.1	s__JABILA01 sp018650465	99.9052	685	719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.90	99.89	0.96	0.95	4	conclusive
GCA_018654745.1	s__JABILA01 sp018654745	80.02	362	719	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__JABILA01	95.0	99.91	99.83	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:53,628] [INFO] GTDB search result was written to OceanDNA-b32650/result_gtdb.tsv
[2023-03-17 23:09:53,628] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:53,630] [INFO] DFAST_QC result json was written to OceanDNA-b32650/dqc_result.json
[2023-03-17 23:09:53,630] [INFO] DFAST_QC completed!
[2023-03-17 23:09:53,631] [INFO] Total running time: 0h1m22s