[2023-03-17 06:30:49,118] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,118] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,118] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference
[2023-03-17 06:30:50,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stgc1e1ff7d-49cf-45bd-b4c0-9a4c52b720cf/OceanDNA-b11566.fa | prodigal -d OceanDNA-b11566/cds.fna -a OceanDNA-b11566/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:57,144] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:57,145] [INFO] Task started: HMMsearch
[2023-03-17 06:30:57,145] [INFO] Running command: hmmsearch --tblout OceanDNA-b11566/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/reference_markers.hmm OceanDNA-b11566/protein.faa > /dev/null
[2023-03-17 06:30:57,324] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:57,324] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc1e1ff7d-49cf-45bd-b4c0-9a4c52b720cf/OceanDNA-b11566.fa]
[2023-03-17 06:30:57,333] [INFO] Query marker FASTA was written to OceanDNA-b11566/markers.fasta
[2023-03-17 06:30:57,333] [INFO] Task started: Blastn
[2023-03-17 06:30:57,333] [INFO] Running command: blastn -query OceanDNA-b11566/markers.fasta -db /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/reference_markers.fasta -out OceanDNA-b11566/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,864] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,865] [INFO] Selected 26 target genomes.
[2023-03-17 06:30:57,865] [INFO] Target genome list was writen to OceanDNA-b11566/target_genomes.txt
[2023-03-17 06:30:57,877] [INFO] Task started: fastANI
[2023-03-17 06:30:57,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1e1ff7d-49cf-45bd-b4c0-9a4c52b720cf/OceanDNA-b11566.fa --refList OceanDNA-b11566/target_genomes.txt --output OceanDNA-b11566/fastani_result.tsv --threads 1
[2023-03-17 06:31:13,315] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:13,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:13,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:13,316] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:13,316] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:13,316] [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 06:31:13,316] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11566/tc_result.tsv
[2023-03-17 06:31:13,317] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:13,317] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:13,317] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/checkm_data
[2023-03-17 06:31:13,319] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:13,321] [INFO] Task started: CheckM
[2023-03-17 06:31:13,322] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11566/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11566/checkm_input OceanDNA-b11566/checkm_result
[2023-03-17 06:31:36,047] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:36,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.19%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:36,049] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:36,049] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:36,049] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11566/markers.fasta)
[2023-03-17 06:31:36,049] [INFO] Task started: Blastn
[2023-03-17 06:31:36,049] [INFO] Running command: blastn -query OceanDNA-b11566/markers.fasta -db /var/lib/cwl/stg9ed13595-06aa-4daf-a951-bb82bcff042e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11566/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:36,875] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:36,875] [INFO] Selected 18 target genomes.
[2023-03-17 06:31:36,876] [INFO] Target genome list was writen to OceanDNA-b11566/target_genomes_gtdb.txt
[2023-03-17 06:31:37,247] [INFO] Task started: fastANI
[2023-03-17 06:31:37,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1e1ff7d-49cf-45bd-b4c0-9a4c52b720cf/OceanDNA-b11566.fa --refList OceanDNA-b11566/target_genomes_gtdb.txt --output OceanDNA-b11566/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:43,753] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:43,759] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 06:31:43,759] [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_002713285.1	s__SP256 sp002713285	80.5593	257	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722215.1	s__SP256 sp002722215	78.1882	181	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698365.1	s__GCA-002707245 sp002698365	77.3826	87	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714185.1	s__SP256 sp002714185	77.3531	159	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__SP256	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707245.1	s__GCA-002707245 sp002707245	77.3193	97	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002707245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701365.1	s__GCA-002701365 sp002701365	76.6413	133	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-002701365	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718895.1	s__GCA-2718895 sp002718895	76.5536	75	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2718895	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002171975.2	s__GCA-2696965 sp002171975	76.2285	93	364	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__TMED113;g__GCA-2696965	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:43,759] [INFO] GTDB search result was written to OceanDNA-b11566/result_gtdb.tsv
[2023-03-17 06:31:43,759] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:43,760] [INFO] DFAST_QC result json was written to OceanDNA-b11566/dqc_result.json
[2023-03-17 06:31:43,760] [INFO] DFAST_QC completed!
[2023-03-17 06:31:43,760] [INFO] Total running time: 0h0m55s