[2023-03-15 05:29:10,769] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:29:10,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:29:10,770] [INFO] DQC Reference Directory: /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference
[2023-03-15 05:29:12,384] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:29:12,384] [INFO] Task started: Prodigal
[2023-03-15 05:29:12,384] [INFO] Running command: cat /var/lib/cwl/stg28aacc7e-bd66-46af-b890-4a7b985a0fb0/OceanDNA-b34787.fa | prodigal -d OceanDNA-b34787/cds.fna -a OceanDNA-b34787/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:29:22,484] [INFO] Task succeeded: Prodigal
[2023-03-15 05:29:22,485] [INFO] Task started: HMMsearch
[2023-03-15 05:29:22,485] [INFO] Running command: hmmsearch --tblout OceanDNA-b34787/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/reference_markers.hmm OceanDNA-b34787/protein.faa > /dev/null
[2023-03-15 05:29:22,712] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:29:22,713] [INFO] Found 6/6 markers.
[2023-03-15 05:29:22,727] [INFO] Query marker FASTA was written to OceanDNA-b34787/markers.fasta
[2023-03-15 05:29:22,727] [INFO] Task started: Blastn
[2023-03-15 05:29:22,727] [INFO] Running command: blastn -query OceanDNA-b34787/markers.fasta -db /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/reference_markers.fasta -out OceanDNA-b34787/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:29:23,319] [INFO] Task succeeded: Blastn
[2023-03-15 05:29:23,320] [INFO] Selected 33 target genomes.
[2023-03-15 05:29:23,320] [INFO] Target genome list was writen to OceanDNA-b34787/target_genomes.txt
[2023-03-15 05:29:23,341] [INFO] Task started: fastANI
[2023-03-15 05:29:23,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg28aacc7e-bd66-46af-b890-4a7b985a0fb0/OceanDNA-b34787.fa --refList OceanDNA-b34787/target_genomes.txt --output OceanDNA-b34787/fastani_result.tsv --threads 1
[2023-03-15 05:29:46,006] [INFO] Task succeeded: fastANI
[2023-03-15 05:29:46,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:29:46,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:29:46,007] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:29:46,007] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:29:46,007] [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 05:29:46,007] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34787/tc_result.tsv
[2023-03-15 05:29:46,007] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:29:46,007] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:29:46,007] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/checkm_data
[2023-03-15 05:29:46,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:29:46,014] [INFO] Task started: CheckM
[2023-03-15 05:29:46,014] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34787/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34787/checkm_input OceanDNA-b34787/checkm_result
[2023-03-15 05:30:15,472] [INFO] Task succeeded: CheckM
[2023-03-15 05:30:15,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:30:15,474] [INFO] ===== Completeness check finished =====
[2023-03-15 05:30:15,474] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:30:15,474] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34787/markers.fasta)
[2023-03-15 05:30:15,474] [INFO] Task started: Blastn
[2023-03-15 05:30:15,474] [INFO] Running command: blastn -query OceanDNA-b34787/markers.fasta -db /var/lib/cwl/stga5e70f8d-a53c-41d4-8d34-f07d65b18038/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34787/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:30:16,284] [INFO] Task succeeded: Blastn
[2023-03-15 05:30:16,285] [INFO] Selected 23 target genomes.
[2023-03-15 05:30:16,285] [INFO] Target genome list was writen to OceanDNA-b34787/target_genomes_gtdb.txt
[2023-03-15 05:30:16,302] [INFO] Task started: fastANI
[2023-03-15 05:30:16,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg28aacc7e-bd66-46af-b890-4a7b985a0fb0/OceanDNA-b34787.fa --refList OceanDNA-b34787/target_genomes_gtdb.txt --output OceanDNA-b34787/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:30:30,358] [INFO] Task succeeded: fastANI
[2023-03-15 05:30:30,362] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:30:30,362] [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_014872805.1	s__Glaciecola sp014872805	95.5826	529	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018623155.1	s__Glaciecola sp018623155	82.3678	399	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292215.1	s__Glaciecola sp002292215	76.897	60	552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.49	98.83	0.91	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-15 05:30:30,362] [INFO] GTDB search result was written to OceanDNA-b34787/result_gtdb.tsv
[2023-03-15 05:30:30,362] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:30:30,363] [INFO] DFAST_QC result json was written to OceanDNA-b34787/dqc_result.json
[2023-03-15 05:30:30,363] [INFO] DFAST_QC completed!
[2023-03-15 05:30:30,363] [INFO] Total running time: 0h1m20s