[2023-03-19 01:25:20,230] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:25:20,230] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:25:20,230] [INFO] DQC Reference Directory: /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference
[2023-03-19 01:25:21,374] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:25:21,374] [INFO] Task started: Prodigal
[2023-03-19 01:25:21,374] [INFO] Running command: cat /var/lib/cwl/stg18e0c560-863c-4171-9885-4a55621b0a4c/OceanDNA-b20495.fa | prodigal -d OceanDNA-b20495/cds.fna -a OceanDNA-b20495/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:25:26,801] [INFO] Task succeeded: Prodigal
[2023-03-19 01:25:26,801] [INFO] Task started: HMMsearch
[2023-03-19 01:25:26,801] [INFO] Running command: hmmsearch --tblout OceanDNA-b20495/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/reference_markers.hmm OceanDNA-b20495/protein.faa > /dev/null
[2023-03-19 01:25:26,975] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:25:26,975] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg18e0c560-863c-4171-9885-4a55621b0a4c/OceanDNA-b20495.fa]
[2023-03-19 01:25:26,987] [INFO] Query marker FASTA was written to OceanDNA-b20495/markers.fasta
[2023-03-19 01:25:26,989] [INFO] Task started: Blastn
[2023-03-19 01:25:26,989] [INFO] Running command: blastn -query OceanDNA-b20495/markers.fasta -db /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/reference_markers.fasta -out OceanDNA-b20495/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:27,534] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:27,536] [INFO] Selected 10 target genomes.
[2023-03-19 01:25:27,536] [INFO] Target genome list was writen to OceanDNA-b20495/target_genomes.txt
[2023-03-19 01:25:27,544] [INFO] Task started: fastANI
[2023-03-19 01:25:27,544] [INFO] Running command: fastANI --query /var/lib/cwl/stg18e0c560-863c-4171-9885-4a55621b0a4c/OceanDNA-b20495.fa --refList OceanDNA-b20495/target_genomes.txt --output OceanDNA-b20495/fastani_result.tsv --threads 1
[2023-03-19 01:25:32,527] [INFO] Task succeeded: fastANI
[2023-03-19 01:25:32,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:25:32,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:25:32,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:25:32,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:25:32,528] [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
--------------------------------------------------------------------------------
[2023-03-19 01:25:32,530] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20495/tc_result.tsv
[2023-03-19 01:25:32,530] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:25:32,530] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:25:32,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/checkm_data
[2023-03-19 01:25:32,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:25:32,544] [INFO] Task started: CheckM
[2023-03-19 01:25:32,544] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20495/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20495/checkm_input OceanDNA-b20495/checkm_result
[2023-03-19 01:25:52,115] [INFO] Task succeeded: CheckM
[2023-03-19 01:25:52,116] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 9.32%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-19 01:25:52,118] [INFO] ===== Completeness check finished =====
[2023-03-19 01:25:52,118] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:25:52,118] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20495/markers.fasta)
[2023-03-19 01:25:52,120] [INFO] Task started: Blastn
[2023-03-19 01:25:52,120] [INFO] Running command: blastn -query OceanDNA-b20495/markers.fasta -db /var/lib/cwl/stg93b666f2-afcc-4627-adf1-86de0b787a1d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20495/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:25:53,000] [INFO] Task succeeded: Blastn
[2023-03-19 01:25:53,002] [INFO] Selected 18 target genomes.
[2023-03-19 01:25:53,002] [INFO] Target genome list was writen to OceanDNA-b20495/target_genomes_gtdb.txt
[2023-03-19 01:25:53,024] [INFO] Task started: fastANI
[2023-03-19 01:25:53,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg18e0c560-863c-4171-9885-4a55621b0a4c/OceanDNA-b20495.fa --refList OceanDNA-b20495/target_genomes_gtdb.txt --output OceanDNA-b20495/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:25:58,230] [INFO] Task succeeded: fastANI
[2023-03-19 01:25:58,235] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:25:58,235] [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_002705605.1	s__GCA-002707645 sp002705605	77.0478	124	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707645.1	s__GCA-002707645 sp002707645	76.9387	94	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704685.1	s__GCA-002707645 sp002704685	76.8778	127	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693365.1	s__GCA-002707645 sp002693365	76.8198	104	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002707645	95.0	98.01	98.01	0.73	0.73	2	-
GCA_002717625.1	s__GCA-2717625 sp002717625	76.1526	65	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-2717625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718585.1	s__GCA-002718585 sp002718585	75.7377	56	370	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-002707645;g__GCA-002718585	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:25:58,236] [INFO] GTDB search result was written to OceanDNA-b20495/result_gtdb.tsv
[2023-03-19 01:25:58,236] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:25:58,238] [INFO] DFAST_QC result json was written to OceanDNA-b20495/dqc_result.json
[2023-03-19 01:25:58,238] [INFO] DFAST_QC completed!
[2023-03-19 01:25:58,238] [INFO] Total running time: 0h0m38s