[2023-03-17 00:26:56,236] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:26:56,237] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:26:56,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference
[2023-03-17 00:26:57,322] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:26:57,323] [INFO] Task started: Prodigal
[2023-03-17 00:26:57,323] [INFO] Running command: cat /var/lib/cwl/stg49bc5336-ecd4-4fb6-bf3b-51ac19d7795c/OceanDNA-b16239.fa | prodigal -d OceanDNA-b16239/cds.fna -a OceanDNA-b16239/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:27:04,921] [INFO] Task succeeded: Prodigal
[2023-03-17 00:27:04,922] [INFO] Task started: HMMsearch
[2023-03-17 00:27:04,922] [INFO] Running command: hmmsearch --tblout OceanDNA-b16239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/reference_markers.hmm OceanDNA-b16239/protein.faa > /dev/null
[2023-03-17 00:27:05,090] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:27:05,091] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg49bc5336-ecd4-4fb6-bf3b-51ac19d7795c/OceanDNA-b16239.fa]
[2023-03-17 00:27:05,100] [INFO] Query marker FASTA was written to OceanDNA-b16239/markers.fasta
[2023-03-17 00:27:05,101] [INFO] Task started: Blastn
[2023-03-17 00:27:05,101] [INFO] Running command: blastn -query OceanDNA-b16239/markers.fasta -db /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/reference_markers.fasta -out OceanDNA-b16239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:27:05,646] [INFO] Task succeeded: Blastn
[2023-03-17 00:27:05,647] [INFO] Selected 20 target genomes.
[2023-03-17 00:27:05,647] [INFO] Target genome list was writen to OceanDNA-b16239/target_genomes.txt
[2023-03-17 00:27:05,653] [INFO] Task started: fastANI
[2023-03-17 00:27:05,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg49bc5336-ecd4-4fb6-bf3b-51ac19d7795c/OceanDNA-b16239.fa --refList OceanDNA-b16239/target_genomes.txt --output OceanDNA-b16239/fastani_result.tsv --threads 1
[2023-03-17 00:30:23,379] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:23,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:30:23,380] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:30:23,380] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:30:23,380] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:30:23,380] [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 00:30:23,380] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16239/tc_result.tsv
[2023-03-17 00:30:23,381] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:30:23,381] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:30:23,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/checkm_data
[2023-03-17 00:30:23,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:30:23,389] [INFO] Task started: CheckM
[2023-03-17 00:30:23,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16239/checkm_input OceanDNA-b16239/checkm_result
[2023-03-17 00:30:48,152] [INFO] Task succeeded: CheckM
[2023-03-17 00:30:48,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.58%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 00:30:48,154] [INFO] ===== Completeness check finished =====
[2023-03-17 00:30:48,154] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:30:48,154] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16239/markers.fasta)
[2023-03-17 00:30:48,156] [INFO] Task started: Blastn
[2023-03-17 00:30:48,156] [INFO] Running command: blastn -query OceanDNA-b16239/markers.fasta -db /var/lib/cwl/stg2869e713-2598-4527-bafc-fa9317d75324/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:30:49,055] [INFO] Task succeeded: Blastn
[2023-03-17 00:30:49,056] [INFO] Selected 24 target genomes.
[2023-03-17 00:30:49,056] [INFO] Target genome list was writen to OceanDNA-b16239/target_genomes_gtdb.txt
[2023-03-17 00:30:49,077] [INFO] Task started: fastANI
[2023-03-17 00:30:49,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg49bc5336-ecd4-4fb6-bf3b-51ac19d7795c/OceanDNA-b16239.fa --refList OceanDNA-b16239/target_genomes_gtdb.txt --output OceanDNA-b16239/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:30:55,533] [INFO] Task succeeded: fastANI
[2023-03-17 00:30:55,538] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:30:55,538] [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_003211755.1	s__AG-363-K07 sp003211755	77.9527	87	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003280295.1	s__AG-363-K07 sp003280295	77.7512	118	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278175.1	s__AG-363-K07 sp003278175	77.195	70	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278225.1	s__AG-363-K07 sp003278225	77.0831	89	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560875.1	s__AG-363-K07 sp902560875	76.9168	63	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003280225.1	s__AG-363-K07 sp003280225	76.7545	70	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-K07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003280345.1	s__AG-363-A16 sp003280345	76.5807	50	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-A16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003280105.1	s__AG-363-N20 sp003280105	76.3302	56	349	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__AG-363-N20	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:30:55,539] [INFO] GTDB search result was written to OceanDNA-b16239/result_gtdb.tsv
[2023-03-17 00:30:55,539] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:30:55,539] [INFO] DFAST_QC result json was written to OceanDNA-b16239/dqc_result.json
[2023-03-17 00:30:55,540] [INFO] DFAST_QC completed!
[2023-03-17 00:30:55,540] [INFO] Total running time: 0h3m59s