[2023-03-14 11:40:05,664] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,664] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference
[2023-03-14 11:40:06,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,761] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,761] [INFO] Running command: cat /var/lib/cwl/stg4a032b1c-6865-41c6-bee1-f9a1ea584a32/OceanDNA-b22059.fa | prodigal -d OceanDNA-b22059/cds.fna -a OceanDNA-b22059/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:32,599] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:32,599] [INFO] Task started: HMMsearch
[2023-03-14 11:40:32,599] [INFO] Running command: hmmsearch --tblout OceanDNA-b22059/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/reference_markers.hmm OceanDNA-b22059/protein.faa > /dev/null
[2023-03-14 11:40:32,845] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:32,846] [INFO] Found 6/6 markers.
[2023-03-14 11:40:32,878] [INFO] Query marker FASTA was written to OceanDNA-b22059/markers.fasta
[2023-03-14 11:40:32,879] [INFO] Task started: Blastn
[2023-03-14 11:40:32,879] [INFO] Running command: blastn -query OceanDNA-b22059/markers.fasta -db /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/reference_markers.fasta -out OceanDNA-b22059/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:33,373] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:33,379] [INFO] Selected 15 target genomes.
[2023-03-14 11:40:33,379] [INFO] Target genome list was writen to OceanDNA-b22059/target_genomes.txt
[2023-03-14 11:40:33,388] [INFO] Task started: fastANI
[2023-03-14 11:40:33,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a032b1c-6865-41c6-bee1-f9a1ea584a32/OceanDNA-b22059.fa --refList OceanDNA-b22059/target_genomes.txt --output OceanDNA-b22059/fastani_result.tsv --threads 1
[2023-03-14 11:40:41,064] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:41,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:41,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:41,064] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:41,064] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:41,064] [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
--------------------------------------------------------------------------------
[2023-03-14 11:40:41,067] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22059/tc_result.tsv
[2023-03-14 11:40:41,072] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:41,072] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:41,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/checkm_data
[2023-03-14 11:40:41,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:41,081] [INFO] Task started: CheckM
[2023-03-14 11:40:41,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22059/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22059/checkm_input OceanDNA-b22059/checkm_result
[2023-03-14 11:41:44,889] [INFO] Task succeeded: CheckM
[2023-03-14 11:41:44,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 9.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:41:44,914] [INFO] ===== Completeness check finished =====
[2023-03-14 11:41:44,914] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:41:44,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22059/markers.fasta)
[2023-03-14 11:41:44,915] [INFO] Task started: Blastn
[2023-03-14 11:41:44,915] [INFO] Running command: blastn -query OceanDNA-b22059/markers.fasta -db /var/lib/cwl/stg88fead8f-e79e-4873-80bf-cfc07aac78e9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22059/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:41:45,588] [INFO] Task succeeded: Blastn
[2023-03-14 11:41:45,597] [INFO] Selected 11 target genomes.
[2023-03-14 11:41:45,597] [INFO] Target genome list was writen to OceanDNA-b22059/target_genomes_gtdb.txt
[2023-03-14 11:41:45,639] [INFO] Task started: fastANI
[2023-03-14 11:41:45,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a032b1c-6865-41c6-bee1-f9a1ea584a32/OceanDNA-b22059.fa --refList OceanDNA-b22059/target_genomes_gtdb.txt --output OceanDNA-b22059/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:53,903] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:53,909] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:41:53,909] [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_018670825.1	s__Scalindua sp018670825	99.8409	1294	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.80	99.75	0.89	0.87	5	conclusive
GCA_007859995.1	s__Scalindua rubra_B	83.7577	564	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.90	99.85	0.94	0.91	3	-
GCA_018648405.1	s__Scalindua sp018648405	82.2293	429	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002443295.1	s__Scalindua japonica	80.8704	680	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263435.1	s__Scalindua arabica	78.6234	366	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001828595.1	s__Scalindua sp001828595	78.502	326	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	99.23	99.13	0.79	0.77	3	-
GCA_001723765.1	s__Scalindua rubra_A	77.1802	297	1581	d__Bacteria;p__Planctomycetota;c__Brocadiae;o__Brocadiales;f__Scalinduaceae;g__Scalindua	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:53,913] [INFO] GTDB search result was written to OceanDNA-b22059/result_gtdb.tsv
[2023-03-14 11:41:53,919] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:53,924] [INFO] DFAST_QC result json was written to OceanDNA-b22059/dqc_result.json
[2023-03-14 11:41:53,924] [INFO] DFAST_QC completed!
[2023-03-14 11:41:53,924] [INFO] Total running time: 0h1m48s