[2023-03-16 01:03:15,341] [INFO] DFAST_QC pipeline started.
[2023-03-16 01:03:15,341] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 01:03:15,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference
[2023-03-16 01:03:16,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 01:03:16,489] [INFO] Task started: Prodigal
[2023-03-16 01:03:16,489] [INFO] Running command: cat /var/lib/cwl/stg48135ca8-edb0-4b24-a47d-c39360852f0a/OceanDNA-b37706.fa | prodigal -d OceanDNA-b37706/cds.fna -a OceanDNA-b37706/protein.faa -g 11 -q > /dev/null
[2023-03-16 01:03:23,919] [INFO] Task succeeded: Prodigal
[2023-03-16 01:03:23,919] [INFO] Task started: HMMsearch
[2023-03-16 01:03:23,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b37706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/reference_markers.hmm OceanDNA-b37706/protein.faa > /dev/null
[2023-03-16 01:03:24,074] [INFO] Task succeeded: HMMsearch
[2023-03-16 01:03:24,075] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg48135ca8-edb0-4b24-a47d-c39360852f0a/OceanDNA-b37706.fa]
[2023-03-16 01:03:24,088] [INFO] Query marker FASTA was written to OceanDNA-b37706/markers.fasta
[2023-03-16 01:03:24,089] [INFO] Task started: Blastn
[2023-03-16 01:03:24,089] [INFO] Running command: blastn -query OceanDNA-b37706/markers.fasta -db /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/reference_markers.fasta -out OceanDNA-b37706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:03:24,631] [INFO] Task succeeded: Blastn
[2023-03-16 01:03:24,632] [INFO] Selected 20 target genomes.
[2023-03-16 01:03:24,633] [INFO] Target genome list was writen to OceanDNA-b37706/target_genomes.txt
[2023-03-16 01:03:24,680] [INFO] Task started: fastANI
[2023-03-16 01:03:24,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg48135ca8-edb0-4b24-a47d-c39360852f0a/OceanDNA-b37706.fa --refList OceanDNA-b37706/target_genomes.txt --output OceanDNA-b37706/fastani_result.tsv --threads 1
[2023-03-16 01:03:37,442] [INFO] Task succeeded: fastANI
[2023-03-16 01:03:37,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 01:03:37,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 01:03:37,443] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 01:03:37,443] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 01:03:37,443] [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
--------------------------------------------------------------------------------
[2023-03-16 01:03:37,443] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37706/tc_result.tsv
[2023-03-16 01:03:37,443] [INFO] ===== Taxonomy check completed =====
[2023-03-16 01:03:37,444] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 01:03:37,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/checkm_data
[2023-03-16 01:03:37,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 01:03:37,450] [INFO] Task started: CheckM
[2023-03-16 01:03:37,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37706/checkm_input OceanDNA-b37706/checkm_result
[2023-03-16 01:04:01,263] [INFO] Task succeeded: CheckM
[2023-03-16 01:04:01,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 01:04:01,267] [INFO] ===== Completeness check finished =====
[2023-03-16 01:04:01,267] [INFO] ===== Start GTDB Search =====
[2023-03-16 01:04:01,267] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37706/markers.fasta)
[2023-03-16 01:04:01,268] [INFO] Task started: Blastn
[2023-03-16 01:04:01,268] [INFO] Running command: blastn -query OceanDNA-b37706/markers.fasta -db /var/lib/cwl/stg220b4644-c551-4460-84ea-4576d31fb7dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 01:04:02,087] [INFO] Task succeeded: Blastn
[2023-03-16 01:04:02,088] [INFO] Selected 16 target genomes.
[2023-03-16 01:04:02,088] [INFO] Target genome list was writen to OceanDNA-b37706/target_genomes_gtdb.txt
[2023-03-16 01:04:02,594] [INFO] Task started: fastANI
[2023-03-16 01:04:02,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg48135ca8-edb0-4b24-a47d-c39360852f0a/OceanDNA-b37706.fa --refList OceanDNA-b37706/target_genomes_gtdb.txt --output OceanDNA-b37706/fastani_result_gtdb.tsv --threads 1
[2023-03-16 01:04:08,323] [INFO] Task succeeded: fastANI
[2023-03-16 01:04:08,328] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 01:04:08,328] [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_002721785.1	s__Luminiphilus sp002721785	90.4048	329	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_902631395.1	s__Luminiphilus sp902631395	81.7196	193	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.59	98.59	0.74	0.74	2	-
GCA_902623175.1	s__Luminiphilus sp902623175	77.0353	70	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	76.9006	62	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523115.1	s__Luminiphilus sp011523115	76.8047	56	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	76.7067	67	359	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 01:04:08,329] [INFO] GTDB search result was written to OceanDNA-b37706/result_gtdb.tsv
[2023-03-16 01:04:08,329] [INFO] ===== GTDB Search completed =====
[2023-03-16 01:04:08,329] [INFO] DFAST_QC result json was written to OceanDNA-b37706/dqc_result.json
[2023-03-16 01:04:08,330] [INFO] DFAST_QC completed!
[2023-03-16 01:04:08,330] [INFO] Total running time: 0h0m53s